Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 19 of 292
Found at i:5074840 original size:23 final size:23
Alignment explanation
Indices: 5074813--5074860 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5074803 AAACACTTTA
5074813 ACCCTTCAATAAATGTAAAACTT
1 ACCCTTCAATAAATGTAAAACTT
5074836 ACCCTTCAATAAATGTAAAACTT
1 ACCCTTCAATAAATGTAAAACTT
5074859 AC
1 AC
5074861 ATTTTTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (23 bp):
ACCCTTCAATAAATGTAAAACTT
Found at i:5076842 original size:18 final size:19
Alignment explanation
Indices: 5076806--5076843 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5076796 GAAAAGCAAC
* *
5076806 AAAATAGAAAAATATATAG
1 AAAATAGAAAAAGAAATAG
5076825 AAAAT-GAAAAAGAAATAG
1 AAAATAGAAAAAGAAATAG
5076843 A
1 A
5076844 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (19 bp):
AAAATAGAAAAAGAAATAG
Found at i:5089718 original size:13 final size:13
Alignment explanation
Indices: 5089700--5089727 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5089690 GTAGAAGTGC
5089700 ATTTGATTTGAGA
1 ATTTGATTTGAGA
5089713 ATTTGATTTGAGA
1 ATTTGATTTGAGA
5089726 AT
1 AT
5089728 AATTCATTAA
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:0.32, C:0.00, G:0.21, T:0.46
Consensus pattern (13 bp):
ATTTGATTTGAGA
Found at i:5092011 original size:16 final size:16
Alignment explanation
Indices: 5091990--5092021 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5091980 AGCTCATGCA
*
5091990 AATTCATGCACGTAAG
1 AATTCATGCACATAAG
5092006 AATTCATGCACATAAG
1 AATTCATGCACATAAG
5092022 TTGTCCGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (16 bp):
AATTCATGCACATAAG
Found at i:5096428 original size:16 final size:16
Alignment explanation
Indices: 5096407--5096437 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5096397 GCTCATGCAG
*
5096407 ATTCATGCACGTAAGA
1 ATTCATGCACATAAGA
5096423 ATTCATGCACATAAG
1 ATTCATGCACATAAG
5096438 TTATCCGGGT
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:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (16 bp):
ATTCATGCACATAAGA
Found at i:5097348 original size:15 final size:15
Alignment explanation
Indices: 5097328--5097366 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
5097318 AAAAAAAAGA
5097328 AGGAGGAGGAAGAGG
1 AGGAGGAGGAAGAGG
*
5097343 AGGAGGAGAAAGAGG
1 AGGAGGAGGAAGAGG
*
5097358 AGGTGGAGG
1 AGGAGGAGG
5097367 TCAACTAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.59, T:0.03
Consensus pattern (15 bp):
AGGAGGAGGAAGAGG
Found at i:5102879 original size:7 final size:7
Alignment explanation
Indices: 5102869--5102942 Score: 57
Period size: 7 Copynumber: 11.1 Consensus size: 7
5102859 TAACTAAAAT
5102869 AAAATAA
1 AAAATAA
5102876 AAAA-AA
1 AAAATAA
*
5102882 ATAATAA
1 AAAATAA
*
5102889 ATAATAA
1 AAAATAA
*
5102896 ATAATAA
1 AAAATAA
*
5102903 AAGA-AA
1 AAAATAA
**
5102909 AAAAGGA
1 AAAATAA
5102916 AAAATAA
1 AAAATAA
*
5102923 ATAA-AA
1 AAAATAA
5102929 AAAAT-A
1 AAAATAA
5102935 AAAATAA
1 AAAATAA
5102942 A
1 A
5102943 GATTGGGTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
6 21 0.39
7 33 0.61
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:5102903 original size:27 final size:25
Alignment explanation
Indices: 5102864--5102942 Score: 83
Period size: 27 Copynumber: 3.1 Consensus size: 25
5102854 ATATTTAACT
5102864 AAAAT-AA-AATAAAAAAAAATAATA
1 AAAATAAATAATAAAAAAAAA-AATA
*
5102888 AATAATAAATAATAAAAGAAAAAAAGGA
1 AA-AATAAATAATAAAA-AAAAAAA-TA
5102916 AAAATAAATAA-AAAAAATAAAAATA
1 AAAATAAATAATAAAAAA-AAAAATA
5102941 AA
1 AA
5102943 GATTGGGTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
24 2 0.04
25 8 0.17
26 11 0.23
27 18 0.38
28 8 0.17
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (25 bp):
AAAATAAATAATAAAAAAAAAAATA
Found at i:5102928 original size:9 final size:10
Alignment explanation
Indices: 5102864--5102942 Score: 67
Period size: 10 Copynumber: 7.8 Consensus size: 10
5102854 ATATTTAACT
5102864 AAAATAAAATA
1 AAAAT-AAATA
*
5102875 AAAAAAAATA
1 AAAATAAATA
5102885 ATAAAT-AATA
1 A-AAATAAATA
5102895 AATAATAAA-A
1 AA-AATAAATA
*
5102905 GAAAA-AAAGGA
1 -AAAATAAA-TA
5102916 AAAATAAATA
1 AAAATAAATA
5102926 AAAA-AAATA
1 AAAATAAATA
5102935 AAAATAAA
1 AAAATAAA
5102943 GATTGGGTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
9 13 0.23
10 29 0.51
11 15 0.26
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (10 bp):
AAAATAAATA
Found at i:5106675 original size:20 final size:20
Alignment explanation
Indices: 5106637--5106684 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5106627 TAAATTCTAA
* **
5106637 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
5106657 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
5106677 AAA-ATAAA
1 AAAGATAAA
5106685 ATCCTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:5107544 original size:27 final size:27
Alignment explanation
Indices: 5107514--5107569 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5107504 TGATCTTTTC
5107514 CTCCTATAATCACTAGAATCAACCCTA
1 CTCCTATAATCACTAGAATCAACCCTA
5107541 CTCCTATAATCACTAGAATCAACCCTA
1 CTCCTATAATCACTAGAATCAACCCTA
5107568 CT
1 CT
5107570 ACTCATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.34, G:0.04, T:0.27
Consensus pattern (27 bp):
CTCCTATAATCACTAGAATCAACCCTA
Found at i:5109329 original size:36 final size:37
Alignment explanation
Indices: 5109275--5109356 Score: 121
Period size: 36 Copynumber: 2.2 Consensus size: 37
5109265 CATAACAATT
* *
5109275 TATTTAAATATATAAACAATCGATTCAAAAGAAATGA
1 TATTTAAATACATAAACAATCGATTCAAAAGAAATAA
*
5109312 TATTTTAATACAT-AACAATCGATTCAAAAGAAATAA
1 TATTTAAATACATAAACAATCGATTCAAAAGAAATAA
5109348 TATTGTAAA
1 TATT-TAAA
5109357 AATCTTAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 26 0.65
37 14 0.35
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (37 bp):
TATTTAAATACATAAACAATCGATTCAAAAGAAATAA
Found at i:5112172 original size:3 final size:3
Alignment explanation
Indices: 5112164--5112193 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5112154 CCCTTTGGTC
5112164 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5112194 TGGTCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5112220 original size:12 final size:12
Alignment explanation
Indices: 5112203--5112264 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
5112193 TTGGTCATAT
*
5112203 TTTATTTTTTTA
1 TTTATTTGTTTA
**
5112215 TTTATTTACTTA
1 TTTATTTGTTTA
* *
5112227 TTCATTTGCTTA
1 TTTATTTGTTTA
*
5112239 TTTCATTTTTCTTA
1 TTT-ATTTGT-TTA
5112253 TTTATTTGTTTA
1 TTTATTTGTTTA
5112265 AGCTTTTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 25 0.62
13 9 0.22
14 6 0.15
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTATTTGTTTA
Found at i:5113274 original size:7 final size:8
Alignment explanation
Indices: 5113245--5113358 Score: 68
Period size: 9 Copynumber: 13.2 Consensus size: 8
5113235 ACAAAGGAAC
5113245 TAATAAAA
1 TAATAAAA
*
5113253 TATTAAAA
1 TAATAAAA
5113261 TAATAAAA
1 TAATAAAA
5113269 -AATAAAAA
1 TAAT-AAAA
* **
5113277 TGAGCAAA
1 TAATAAAA
5113285 TAGATAAAA
1 TA-ATAAAA
** *
5113294 GGATACGAA
1 TAATA-AAA
*
5113303 TAAAACAAA
1 TAATA-AAA
5113312 TAATAATAA
1 TAATAA-AA
5113321 TAATAATAA
1 TAATAA-AA
5113330 TAATAATAA
1 TAATAA-AA
5113339 TAATAATAA
1 TAATAA-AA
5113348 TAATAATAA
1 TAATAA-AA
5113357 TA
1 TA
5113359 TGAGTACTAA
Statistics
Matches: 85, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
7 3 0.04
8 26 0.31
9 56 0.66
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (8 bp):
TAATAAAA
Found at i:5113318 original size:3 final size:3
Alignment explanation
Indices: 5113310--5113358 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
5113300 GAATAAAACA
5113310 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5113358 A
1 A
5113359 TGAGTACTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5116759 original size:12 final size:12
Alignment explanation
Indices: 5116742--5116774 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
5116732 CGGCCCGCCC
5116742 ATATTAATTTTT
1 ATATTAATTTTT
5116754 ATATT-ATTTTT
1 ATATTAATTTTT
5116765 ATA-TAATTTT
1 ATATTAATTTT
5116775 AAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:5116817 original size:17 final size:18
Alignment explanation
Indices: 5116776--5116815 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5116766 TATAATTTTA
*
5116776 AAAAATATATAAACTATC
1 AAAAATATACAAACTATC
5116794 AAAAATACTACAAAC-ATC
1 AAAAATA-TACAAACTATC
5116812 AAAA
1 AAAA
5116816 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATATACAAACTATC
Found at i:5116932 original size:30 final size:30
Alignment explanation
Indices: 5116896--5116956 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
5116886 TAATTTAACA
* *
5116896 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATACCTCTAAAATAATAAAAAAATT
* *
5116926 AGCAAATATCTTTAAAATAATAAAAAAATT
1 AGCAAATACCTCTAAAATAATAAAAAAATT
5116956 A
1 A
5116957 ACAATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.26
Consensus pattern (30 bp):
AGCAAATACCTCTAAAATAATAAAAAAATT
Found at i:5117428 original size:47 final size:47
Alignment explanation
Indices: 5117359--5117452 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
5117349 TTATAGAAGG
* *
5117359 GAAGACCTTGACTTCCAAAGCAATAAACTTTGTTTAAGTTGGATTAA
1 GAAGACCTTGACTTCCAAAGCAATAAACTTTGTTTAAATTCGATTAA
5117406 GAAGACCTTGACTTCCAAAGCAATAAACTTTGTTTAAATTCGATTAA
1 GAAGACCTTGACTTCCAAAGCAATAAACTTTGTTTAAATTCGATTAA
5117453 CTTATTAGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (47 bp):
GAAGACCTTGACTTCCAAAGCAATAAACTTTGTTTAAATTCGATTAA
Found at i:5118051 original size:72 final size:72
Alignment explanation
Indices: 5117890--5118051 Score: 209
Period size: 72 Copynumber: 2.2 Consensus size: 72
5117880 GAAGAGTTTG
* ** * * *
5117890 AAACAGTTGGACCTATCCAATAACCAAATTCTTGGTCCCATTCCTTCTACCTTGGGCAACTTAAC
1 AAACAGTTGGACCTATCCAAAAACCAAATTAGTGGTCCCATCCCTTCTACCTTAGGCAAATTAAC
*
5117955 CACTTTA
66 CAATTTA
* **
5117962 AAA-ATGTTGAACCTATCCAAAAACCAAATTAGTGGTCGTATCCCTTCTACCTTAGGCAAATTAA
1 AAACA-GTTGGACCTATCCAAAAACCAAATTAGTGGTCCCATCCCTTCTACCTTAGGCAAATTAA
5118026 CCAATTTA
65 CCAATTTA
*
5118034 AAACAGTTGGACTTATCC
1 AAACAGTTGGACCTATCC
5118052 TTCAATCAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
71 1 0.01
72 74 0.97
73 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (72 bp):
AAACAGTTGGACCTATCCAAAAACCAAATTAGTGGTCCCATCCCTTCTACCTTAGGCAAATTAAC
CAATTTA
Found at i:5121841 original size:19 final size:20
Alignment explanation
Indices: 5121819--5121856 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5121809 TTAAAAAACC
*
5121819 TAAA-AAACCCCAAGCCCAT
1 TAAATAAACCCAAAGCCCAT
5121838 TAAATAAACCCAAAGCCCA
1 TAAATAAACCCAAAGCCCA
5121857 AACCTTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.34, G:0.05, T:0.11
Consensus pattern (20 bp):
TAAATAAACCCAAAGCCCAT
Found at i:5122885 original size:3 final size:3
Alignment explanation
Indices: 5122877--5123393 Score: 193
Period size: 3 Copynumber: 174.0 Consensus size: 3
5122867 ATTAAATATG
* * *
5122877 TTA TTA TTA TTA CTA TTA TTA TT- TTA CTA TTA TTA TCTA ATA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* * * * *
5122921 TT- TTA TTA TCA TTAA TTA TTA TTA CTA TTA CTA TTA TTC TTA TAA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
5122966 ACA -TA TTA TTA TTA TTT TTA TTA -TA TTA TTA TT- TCCTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA
* * **
5123010 TTA CTA TTA TTA TTA TTG TTA TTA ACA TATA TTA TTA TTA TTAA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A T-TA
* * * * * * * *
5123058 TTG TTA CTC TCTA TTA CTA TTA TTA TTA -TC TTA GTA TTA -AA CTAA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * *
5123103 TTAA TT- TCA -TA TTG TTA TTA TTA -TA TTA TATA TT- TTC TT- TTT
1 TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* ** * *
5123145 TTG TGT- TTA TT- TGC TTA TTA TT- TTA TTA TTA AT- TTA GTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * ** * *
5123187 TTAA CTA TTTA TTA TTA TCC TTA GTA ACA -TA TCA TCA TT- TTA TTA
1 TT-A TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * *
5123232 TTA ATA TATA TGA TTA TTA CTC TTG TTA TTT TCTA CTT- TGA CTTG TT-
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA -TTA TTA
* *
5123279 GTA CTA 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 TTA
* * * *
5123327 TTA TTA TCT- TTA TTA CTA TTA CTA CTA TTA TTA CTA -TA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5123371 TTA TT- TCTA -TA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
5123394 CTAACATATT
Statistics
Matches: 382, Mismatches: 87, Indels: 90
0.68 0.16 0.16
Matches are distributed among these distances:
2 36 0.09
3 309 0.81
4 34 0.09
5 3 0.01
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:5122976 original size:68 final size:65
Alignment explanation
Indices: 5122904--5123047 Score: 173
Period size: 68 Copynumber: 2.1 Consensus size: 65
5122894 ATTATTTTAC
*
5122904 TATTATTATCTAATATATT-TTATTATCATTAATTATTATTACTATTACTATTATTCTTATAAAC
1 TATTATTATCTAATATATTATTATT-TC-CT-ATTATTATTACTATTACTATTATTCTTATAAAC
5122968 ATA
63 ATA
* * * * *
5122971 TTATTATTATTTTTATTATATTATTATTTCCTATTATTATTACTATTATTATTATTGTTATTAAC
1 -TATTATTA--TCTAATATATTATTATTTCCTATTATTATTACTATTACTATTATTCTTATAAAC
5123036 ATA
63 ATA
5123039 TATTATTAT
1 TATTATTAT
5123048 TATTAATGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
65 1 0.01
67 8 0.12
68 41 0.61
69 1 0.01
70 11 0.16
71 5 0.07
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (65 bp):
TATTATTATCTAATATATTATTATTTCCTATTATTATTACTATTACTATTATTCTTATAAACATA
Found at i:5137208 original size:3 final size:3
Alignment explanation
Indices: 5137200--5137251 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
5137190 TTAGTTTCTT
5137200 TTA 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 TTA
5137248 TTA T
1 TTA T
5137252 CTCTTAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5139592 original size:13 final size:13
Alignment explanation
Indices: 5139567--5139601 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5139557 CAATTCCAAT
5139567 TTCAGATATCAGA
1 TTCAGATATCAGA
5139580 TTACAGA-ATCAGA
1 TT-CAGATATCAGA
5139593 TTCAGATAT
1 TTCAGATAT
5139602 GCAAAATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.20
13 12 0.60
14 4 0.20
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
TTCAGATATCAGA
Found at i:5139609 original size:20 final size:20
Alignment explanation
Indices: 5139568--5139609 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5139558 AATTCCAATT
*
5139568 TCAGATATCAGATTACAGAA
1 TCAGATATCAGATTACAAAA
*
5139588 TCAGAT-TCAGATATGCAAAA
1 TCAGATATCAGAT-TACAAAA
5139608 TC
1 TC
5139610 CTAACCCCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (20 bp):
TCAGATATCAGATTACAAAA
Found at i:5140197 original size:32 final size:32
Alignment explanation
Indices: 5140161--5140255 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
5140151 GCCGGCACGT
*
5140161 CCAACTTGGCCTTGCCCGTGTAGCCCACATTC
1 CCAACTTGGCCTTGCCCGTGTAGCCCACATGC
5140193 CCAACTTGGCCTTGCCCGTGTAGCCCACATGC
1 CCAACTTGGCCTTGCCCGTGTAGCCCACATGC
* *
5140225 CCAACTTGGCCTAGCCCGTGTGGCCCACATG
1 CCAACTTGGCCTTGCCCGTGTAGCCCACATG
5140256 GCCACATTGG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.16, C:0.40, G:0.22, T:0.22
Consensus pattern (32 bp):
CCAACTTGGCCTTGCCCGTGTAGCCCACATGC
Found at i:5148763 original size:8 final size:8
Alignment explanation
Indices: 5148750--5148774 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5148740 TTACGCTCTA
5148750 TCACAAAC
1 TCACAAAC
5148758 TCACAAAC
1 TCACAAAC
5148766 TCACAAAC
1 TCACAAAC
5148774 T
1 T
5148775 ATCCATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (8 bp):
TCACAAAC
Found at i:5149327 original size:17 final size:18
Alignment explanation
Indices: 5149284--5149343 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
5149274 ACTGGGCATT
*
5149284 TAATCAATTATTAGAATAG
1 TAATCAATTATTAGAA-AA
5149303 TAAT-AATT-TTAGAAAA
1 TAATCAATTATTAGAAAA
*
5149319 TAATCAATTAATA-AAAA
1 TAATCAATTATTAGAAAA
5149336 TAA-CAATT
1 TAATCAATT
5149344 TAACAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 10 0.27
17 17 0.46
18 6 0.16
19 4 0.11
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (18 bp):
TAATCAATTATTAGAAAA
Found at i:5153603 original size:12 final size:12
Alignment explanation
Indices: 5153563--5153606 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
5153553 AAAATTGTTT
5153563 TATT-TTTTATA
1 TATTATTTTATA
5153574 TTATTACTTTTCATA
1 -TATTA-TTTT-ATA
5153589 TATTATTTTATA
1 TATTATTTTATA
5153601 TATTAT
1 TATTAT
5153607 AAGTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 13 0.45
13 4 0.14
14 9 0.31
15 3 0.10
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTATTTTATA
Found at i:5155104 original size:17 final size:15
Alignment explanation
Indices: 5155068--5155098 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5155058 GATAATAGAG
5155068 TAACAAACTCTATAC
1 TAACAAACTCTATAC
*
5155083 TAACAATCTCTATAC
1 TAACAAACTCTATAC
5155098 T
1 T
5155099 CTAACATTCA
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:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (15 bp):
TAACAAACTCTATAC
Found at i:5157103 original size:25 final size:27
Alignment explanation
Indices: 5157066--5157118 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5157056 TCAAACATGC
5157066 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
5157092 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
5157118 A
1 A
5157119 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:5158634 original size:26 final size:26
Alignment explanation
Indices: 5158605--5158712 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
5158595 TGAAATGCCC
5158605 ATCATGGAACATTTACCTGAA-CCATT
1 ATCATGGAACATTTACCT-AACCCATT
5158631 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
5158657 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
5158683 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5158709 ATCA
1 ATCA
5158713 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 2 0.03
26 75 0.97
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5165782 original size:43 final size:43
Alignment explanation
Indices: 5165590--5165792 Score: 207
Period size: 43 Copynumber: 4.7 Consensus size: 43
5165580 TATGTGATTT
* * *
5165590 CATGTAAGACCATGTCTGGGACATTAGCATTG-TAT-TGAGATTA
1 CATGTAAGACCATGTCTGGGACAGTGGCATTGATATAT--GATAA
* * * * * *
5165633 CGTGTAAGACCATGTCTGAGACATTGGCATCGTTA-ATAGATTA
1 CATGTAAGACCATGTCTGGGACAGTGGCATTGATATAT-GATAA
** * *
5165676 TGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATATGATAA
1 CATGTAAGACCATGTCTGGGACAGTGGCATTGATATATGATAA
5165719 CATGTAAGACCATGTCTGGGACAGTGGCATTGATATATGATAA
1 CATGTAAGACCATGTCTGGGACAGTGGCATTGATATATGATAA
* * *
5165762 CATGTAAGACCATATTTGGGATA-TGGCATTG
1 CATGTAAGACCATGTCTGGGACAGTGGCATTG
5165793 TATGAACTTA
Statistics
Matches: 140, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
42 8 0.06
43 127 0.91
44 5 0.04
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (43 bp):
CATGTAAGACCATGTCTGGGACAGTGGCATTGATATATGATAA
Found at i:5171749 original size:5 final size:5
Alignment explanation
Indices: 5171739--5171780 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
5171729 ATGTAAGAAC
* *
5171739 ATAAA ATAAA ATAAA ATAAA ATAAA GTAGAA ATAAA ACAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA-AA ATAAA ATAAA A
5171781 GAAGAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:5171759 original size:15 final size:16
Alignment explanation
Indices: 5171734--5171780 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
5171724 TGAGAATGTA
5171734 AGAACATAAAATAAAAT
1 AGAA-ATAAAATAAAAT
*
5171751 A-AAATAAAATAAAGT
1 AGAAATAAAATAAAAT
*
5171766 AGAAATAAAACAAAA
1 AGAAATAAAATAAAA
5171781 GAAGAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 12 0.46
16 13 0.50
17 1 0.04
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.15
Consensus pattern (16 bp):
AGAAATAAAATAAAAT
Found at i:5176196 original size:17 final size:15
Alignment explanation
Indices: 5176160--5176190 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5176150 GATAACAGAG
5176160 TAACAAACTCTATAC
1 TAACAAACTCTATAC
*
5176175 TAACAATCTCTATAC
1 TAACAAACTCTATAC
5176190 T
1 T
5176191 CTAACATTGA
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:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (15 bp):
TAACAAACTCTATAC
Found at i:5188476 original size:9 final size:9
Alignment explanation
Indices: 5188462--5188487 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5188452 AGCATAATAC
5188462 AAAAATATT
1 AAAAATATT
5188471 AAAAATATT
1 AAAAATATT
5188480 AAAAATAT
1 AAAAATAT
5188488 ATACCATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATATT
Found at i:5188525 original size:14 final size:14
Alignment explanation
Indices: 5188506--5188532 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5188496 TTGTAATGAA
5188506 ATATATAAATATAT
1 ATATATAAATATAT
5188520 ATATATAAATATA
1 ATATATAAATATA
5188533 AAACCAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATAAATATAT
Found at i:5190001 original size:42 final size:42
Alignment explanation
Indices: 5189954--5190041 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
5189944 AATAAATCAA
*
5189954 GAAAATAAATGAATAATAGCTAAAAAGCGAACCAATAC-CTAG
1 GAAAATAAATGAATAATAACTAAAAAGCGAACCAATACTC-AG
*
5189996 GAAAATAAATGAATAATAACTAAGAAGCGAACCAATACTCAG
1 GAAAATAAATGAATAATAACTAAAAAGCGAACCAATACTCAG
5190038 GAAA
1 GAAA
5190042 GAATCCACCT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 42 0.98
43 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.15, T:0.16
Consensus pattern (42 bp):
GAAAATAAATGAATAATAACTAAAAAGCGAACCAATACTCAG
Found at i:5191669 original size:3 final size:3
Alignment explanation
Indices: 5191661--5191695 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5191651 TTTTTTAATT
5191661 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5191696 GAGAACAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5192241 original size:17 final size:16
Alignment explanation
Indices: 5192210--5192241 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5192200 ATGTTTATCT
*
5192210 ACAAATTAATTAAAAA
1 ACAAAATAATTAAAAA
5192226 ACAAAATAATTAAAAA
1 ACAAAATAATTAAAAA
5192242 TCCCAAATCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (16 bp):
ACAAAATAATTAAAAA
Found at i:5205744 original size:23 final size:22
Alignment explanation
Indices: 5205701--5205776 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
5205691 AAAAGGTATC
* *
5205701 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
5205722 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
5205745 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
5205764 TAC-AATCATATCT
1 TACAAATCATATCT
5205777 AAGATTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
18 6 0.14
19 10 0.23
21 3 0.07
22 15 0.34
23 10 0.23
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:5205761 original size:19 final size:19
Alignment explanation
Indices: 5205737--5205827 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
5205727 AATCATATCT
5205737 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
5205756 TCTAAGATTACA-ATCATA
1 TCTAAGATTGCATATCATA
5205774 TCTAAGATT--ATATCATA
1 TCTAAGATTGCATATCATA
*
5205791 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATATCATA
5205810 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
5205828 TGAAGATTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.02
17 15 0.23
18 15 0.23
19 35 0.53
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5205805 original size:54 final size:53
Alignment explanation
Indices: 5205737--5205839 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 53
5205727 AATCATATCT
* *
5205737 TCTAAGATTGCATATCATATCTAAGATTACA-ATCATATCTAAGATTATATCATA
1 TCTAAGATTGCATATCACATCTAAGATTACATATCAT-T-GAAGATTATATCATA
*
5205791 TCTAAGATTGCATATCACATCTAAGATTGCATATCATTGAAGATTATAT
1 TCTAAGATTGCATATCACATCTAAGATTACATATCATTGAAGATTATAT
5205840 TTCCATATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
53 10 0.22
54 30 0.67
55 5 0.11
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (53 bp):
TCTAAGATTGCATATCACATCTAAGATTACATATCATTGAAGATTATATCATA
Found at i:5206235 original size:45 final size:45
Alignment explanation
Indices: 5206180--5206381 Score: 187
Period size: 45 Copynumber: 4.5 Consensus size: 45
5206170 GGAATGCGAT
* * *
5206180 ATCTACTATCTTTGATCTGCTTCCCGTCTAATACAAAGACGCCAA
1 ATCTATTATCTTCGATCTGCTTCCCGTCTAATACAAAGATGCCAA
* * *
5206225 ATCTATTATCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAA
1 ATCTATTATCTTCGATCTGCTTCCCGTCTAATACAAAGATGCC-AA
* * * *
5206271 AT-T-TTTTCTTC-AACTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTATTATCTTCGATC-TGCTTCCCGTCTAATACAAAGATGCCAA
* * * **
5206314 ATCTGTTATCTCCGATTTGC-TCATTGTCTAATACAAAGATGCCAA
1 ATCTATTATCTTCGATCTGCTTC-CCGTCTAATACAAAGATGCCAA
* * *
5206359 ATCTGTCATCTTGGATCTGCTTC
1 ATCTATTATCTTCGATCTGCTTC
5206382 GATGTAAACA
Statistics
Matches: 129, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
43 6 0.05
44 34 0.26
45 82 0.64
46 7 0.05
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (45 bp):
ATCTATTATCTTCGATCTGCTTCCCGTCTAATACAAAGATGCCAA
Found at i:5206323 original size:89 final size:89
Alignment explanation
Indices: 5206197--5206359 Score: 227
Period size: 89 Copynumber: 1.8 Consensus size: 89
5206187 ATCTTTGATC
* * * * *
5206197 TGCTTCCCGTCTAATACAAAGACGCCAAATCTATTATCTTCGATCTGCTCCCCGTCTAATATAGA
1 TGCTCCCCGTCTAATACAAAGACGCCAAATCTATTATCTCCGATCTGCTCACCGTCTAATACAAA
5206262 GATGCCAAAATTTTTTCTTCAACT
66 GATGCCAAAATTTTTTCTTCAACT
* * * * **
5206286 TGCTCCCCGTCTAATACAGAGATGCCAAATCTGTTATCTCCGATTTGCTCATTGTCTAATACAAA
1 TGCTCCCCGTCTAATACAAAGACGCCAAATCTATTATCTCCGATCTGCTCACCGTCTAATACAAA
5206351 GATGCCAAA
66 GATGCCAAA
5206360 TCTGTCATCT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 63 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (89 bp):
TGCTCCCCGTCTAATACAAAGACGCCAAATCTATTATCTCCGATCTGCTCACCGTCTAATACAAA
GATGCCAAAATTTTTTCTTCAACT
Found at i:5206522 original size:78 final size:78
Alignment explanation
Indices: 5206393--5206780 Score: 586
Period size: 78 Copynumber: 5.0 Consensus size: 78
5206383 ATGTAAACAC
*
5206393 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
5206458 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* *
5206471 ATGAAGGTCCA-ATTTGTTATGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCAT-
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATC
* *
5206534 TTGGATCTACTTAA
65 TTGGATCTGCTTCA
*
5206548 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
5206613 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * *
5206626 ATGAAAGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATC
5206690 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * * * *
5206704 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCTCTAAC-AATACAGAGACGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
*
5206768 TAGATCTGCTTCA
66 TGGATCTGCTTCA
5206781 GCGTAAACAC
Statistics
Matches: 280, Mismatches: 25, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
76 2 0.01
77 104 0.37
78 170 0.61
79 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:5206677 original size:155 final size:156
Alignment explanation
Indices: 5206393--5206780 Score: 645
Period size: 155 Copynumber: 2.5 Consensus size: 156
5206383 ATGTAAACAC
* *
5206393 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
* *
5206458 TGGATCTGCTTCAATGAAGGTCCAATTTGTTATGTCTTCGATCTGCTCCCCATCTAATACAGAGA
66 TGGATCTGCTTCAATGAAAGTCCAATCTGTTATGTCTTCGATCTGCTCCCCATCTAATACAGAGA
5206523 TGCCAAATCAT-TTGGATCTACTTAA
131 TGCCAAATCATCTTGGATCTACTTAA
5206548 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
* *
5206613 TGGATCTGCTTCAATGAAAGTCCAATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATATAGAGA
66 TGGATCTGCTTCAATGAAAGTCCAATCTGTTATGTCTTCGATCTGCTCCCCATCTAATACAGAGA
* *
5206678 TGCCAAATCATCTTGGATCTGCTTCA
131 TGCCAAATCATCTTGGATCTACTTAA
* * * *
5206704 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCTCTAAC-AATACAGAGACGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
*
5206768 TAGATCTGCTTCA
66 TGGATCTGCTTCA
5206781 GCGTAAACAC
Statistics
Matches: 219, Mismatches: 13, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
155 169 0.77
156 50 0.23
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (156 bp):
ATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCAATGAAAGTCCAATCTGTTATGTCTTCGATCTGCTCCCCATCTAATACAGAGA
TGCCAAATCATCTTGGATCTACTTAA
Found at i:5206869 original size:44 final size:44
Alignment explanation
Indices: 5206798--5207237 Score: 276
Period size: 44 Copynumber: 10.2 Consensus size: 44
5206788 CACGTGAAAA
*
5206798 CCAAATCTGCTATGTCTTCGATTTGCTCTCTGACAATACAGAGATG
1 CCAAATCTGCTA--TCTTCGATCTGCTCTCTGACAATACAGAGATG
5206844 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGACT-
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGA-TG
* * * * *
5206888 CCAAA--T-C-ATCTTAGATTTGCT-TCAG-CGTAA-ACACGTGAAAG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGAC--AATACA-GAG-ATG
* ** * * *
5206929 CCAAATCTGTTATATCTTTAATTTACTCTCTGACAATACAAAGATG
1 CCAAATCTG--CTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* * * * *
5206975 TCGAATCTGCTATCTTTGATCTGCTTTCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* * * * * *
5207019 TCAAA--T-C-ATCTTAGATCTACT-TC-AACGTAA-ACACGTGAAAG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGAC--AATACA-GAG-ATG
* * * *
5207060 CCAAATCTACTATATCTTCAATTTACTCTCTGACAATACAGAGATG
1 CCAAATCTGC--TATCTTCGATCTGCTCTCTGACAATACAGAGATG
*
5207106 TCAAATCTGCTATCTTCGATCTG----CT--C-ATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* * *
5207143 CCAAATCTACTATCTTCGATCTGCCCTCTAACAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
* * * *
5207187 CCAAATTTGCTATCTTTGATCTGCTCCCTGACAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
5207231 CCAAATC
1 CCAAATC
5207238 ATCTTAGATC
Statistics
Matches: 308, Mismatches: 51, Indels: 72
0.71 0.12 0.17
Matches are distributed among these distances:
37 32 0.10
38 4 0.01
39 11 0.04
40 34 0.11
41 16 0.05
42 2 0.01
43 3 0.01
44 131 0.43
45 1 0.00
46 31 0.10
47 29 0.09
48 11 0.04
49 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (44 bp):
CCAAATCTGCTATCTTCGATCTGCTCTCTGACAATACAGAGATG
Found at i:5206959 original size:131 final size:131
Alignment explanation
Indices: 5206725--5207131 Score: 645
Period size: 131 Copynumber: 3.1 Consensus size: 131
5206715 ATCTGCTGTG
* *
5206725 TCTTCGATCTGCTCTCTAACAATACAGAGACGCCAAATCATCTTAGATCTGCTTCAGCGTAAACA
1 TCTTCGATCTGCTCTCTGACAATACAGAGACTCCAAATCATCTTAGATCTGCTTCAGCGTAAACA
* * * * *
5206790 CGTGAAAACCAAATCTGCTATGTCTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCTGCT
66 CGTGAAAGCCAAATCTGCTATATCTTCAATTTACTCTCTGACAATACAGAGATGTCAAATCTGCT
5206855 A
131 A
*
5206856 TCTTCGATCTGCTCTCTGACAATACAGAGACTCCAAATCATCTTAGATTTGCTTCAGCGTAAACA
1 TCTTCGATCTGCTCTCTGACAATACAGAGACTCCAAATCATCTTAGATCTGCTTCAGCGTAAACA
* * * *
5206921 CGTGAAAGCCAAATCTGTTATATCTTTAATTTACTCTCTGACAATACAAAGATGTCGAATCTGCT
66 CGTGAAAGCCAAATCTGCTATATCTTCAATTTACTCTCTGACAATACAGAGATGTCAAATCTGCT
5206986 A
131 A
* * * *
5206987 TCTTTGATCTGCTTTCTGACAATACAGAGACGT-CAAATCATCTTAGATCTACTTCAACGTAAAC
1 TCTTCGATCTGCTCTCTGACAATACAGAGAC-TCCAAATCATCTTAGATCTGCTTCAGCGTAAAC
*
5207051 ACGTGAAAGCCAAATCTACTATATCTTCAATTTACTCTCTGACAATACAGAGATGTCAAATCTGC
65 ACGTGAAAGCCAAATCTGCTATATCTTCAATTTACTCTCTGACAATACAGAGATGTCAAATCTGC
5207116 TA
130 TA
5207118 TCTTCGATCTGCTC
1 TCTTCGATCTGCTC
5207132 ATACAGAGAT
Statistics
Matches: 251, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
131 250 1.00
132 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (131 bp):
TCTTCGATCTGCTCTCTGACAATACAGAGACTCCAAATCATCTTAGATCTGCTTCAGCGTAAACA
CGTGAAAGCCAAATCTGCTATATCTTCAATTTACTCTCTGACAATACAGAGATGTCAAATCTGCT
A
Found at i:5207148 original size:37 final size:38
Alignment explanation
Indices: 5207093--5207212 Score: 143
Period size: 37 Copynumber: 3.0 Consensus size: 38
5207083 TACTCTCTGA
*
5207093 CAATACAGAGATGTCAAATCTGCTATCTTCGATCTGCT
1 CAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCT
*
5207131 C-ATACAGAGATGCCAAATCTACTATCTTCGATCTGCCCTCT
1 CAATACAGAGATGCCAAATCTGCTATCTTCGATCTG----CT
* *
5207172 AACAATACAGAGATGCCAAATTTGCTATCTTTGATCTGCT
1 --CAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCT
5207212 C
1 C
5207213 CCTGACAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
37 32 0.46
38 2 0.03
40 2 0.03
41 2 0.03
43 1 0.01
44 31 0.44
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (38 bp):
CAATACAGAGATGCCAAATCTGCTATCTTCGATCTGCT
Found at i:5207198 original size:81 final size:82
Alignment explanation
Indices: 5207059--5207212 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 82
5207049 ACACGTGAAA
* * * *
5207059 GCCAAATCTACTATATCTTCAATTTACTCTCTGACAATACAGAGATGTCAAATCTGCTATCTTCG
1 GCCAAATCTAC-ATATCTTCAATCTACCCTCTAACAATACAGAGATGCCAAATCTGCTATCTTCG
5207124 ATCTGCTCATACAGAGAT
65 ATCTGCTCATACAGAGAT
* * * *
5207142 GCCAAATCTAC-TATCTTCGATCTGCCCTCTAACAATACAGAGATGCCAAATTTGCTATCTTTGA
1 GCCAAATCTACATATCTTCAATCTACCCTCTAACAATACAGAGATGCCAAATCTGCTATCTTCGA
5207206 TCTGCTC
66 TCTGCTC
5207213 CCTGACAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 52 0.83
83 11 0.17
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (82 bp):
GCCAAATCTACATATCTTCAATCTACCCTCTAACAATACAGAGATGCCAAATCTGCTATCTTCGA
TCTGCTCATACAGAGAT
Found at i:5212184 original size:12 final size:12
Alignment explanation
Indices: 5212167--5212191 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5212157 GTGACCCTCT
5212167 TCTTTCTTTCTC
1 TCTTTCTTTCTC
5212179 TCTTTCTTTCTC
1 TCTTTCTTTCTC
5212191 T
1 T
5212192 TTTTAACCTT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTTTCTTTCTC
Found at i:5215623 original size:17 final size:17
Alignment explanation
Indices: 5215589--5215652 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
5215579 AATCATATCT
*
5215589 TCTAAGATATGCATCATA
1 TCTAAGAT-TGTATCATA
5215607 TCTAAGATTGTATCATA
1 TCTAAGATTGTATCATA
*
5215624 TCTAAGATTGCATATCACA
1 TCTAAGATTG--TATCATA
5215643 TCTAAGATTG
1 TCTAAGATTG
5215653 CATATCATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
17 18 0.43
18 8 0.19
19 16 0.38
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (17 bp):
TCTAAGATTGTATCATA
Found at i:5215645 original size:19 final size:18
Alignment explanation
Indices: 5215589--5215660 Score: 94
Period size: 19 Copynumber: 3.9 Consensus size: 18
5215579 AATCATATCT
5215589 TCTAAGATATGC-ATCATA
1 TCTAAGAT-TGCTATCATA
5215607 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
5215624 TCTAAGATTGCATATCACA
1 TCTAAGATTGC-TATCATA
5215643 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
5215661 TGAAGATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
17 18 0.37
18 8 0.16
19 23 0.47
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:5216015 original size:6 final size:6
Alignment explanation
Indices: 5216004--5216038 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
5215994 GGGCCTATAT
5216004 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
5216039 ATAATACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:5218314 original size:6 final size:6
Alignment explanation
Indices: 5218305--5218330 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5218295 AAAAAAGAAA
5218305 ATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT AT
5218331 GTAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATAAAT
Found at i:5228699 original size:18 final size:18
Alignment explanation
Indices: 5228641--5228712 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 18
5228631 CCCAACTACT
* *
5228641 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTACC
* * **
5228659 GTATATGTAAATAGTGTC
1 GTATACGTGAATAGTACC
* *
5228677 ATATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
5228695 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
5228713 TTAAACGGTC
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:5233614 original size:2 final size:2
Alignment explanation
Indices: 5233609--5233634 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5233599 TTTACACACT
5233609 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
5233635 CAAATTTTAC
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:5235653 original size:32 final size:33
Alignment explanation
Indices: 5235591--5235662 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
5235581 TATTTTTTAG
5235591 TATTTAGATGAATCTGTATAAAATAATTTCTGA-
1 TATTTAGATGAATCTGTATAAAATAATTTCT-AT
* * *
5235624 TATTTAGATTAATCT-TGTAAAATATTTTCTAT
1 TATTTAGATGAATCTGTATAAAATAATTTCTAT
5235656 TATTTAG
1 TATTTAG
5235663 TAGATTTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 1 0.03
32 20 0.57
33 14 0.40
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.49
Consensus pattern (33 bp):
TATTTAGATGAATCTGTATAAAATAATTTCTAT
Found at i:5236040 original size:15 final size:15
Alignment explanation
Indices: 5236020--5236071 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
5236010 ACTACAAAAC
5236020 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
5236035 ATTTATAATTTTAATAATT
1 ATTTAT--TATTAAT-A-T
*
5236054 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
5236069 ATT
1 ATT
5236072 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 10 0.33
16 1 0.03
17 11 0.37
18 1 0.03
19 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:5236179 original size:16 final size:16
Alignment explanation
Indices: 5236113--5236190 Score: 52
Period size: 16 Copynumber: 4.8 Consensus size: 16
5236103 ATACTATTTA
*
5236113 AATTTATTATTTTTAA-
1 AATTTATTA-TTTAAAT
*
5236129 AATTTATTATTAAAAT
1 AATTTATTATTTAAAT
* **
5236145 AAAATTAAAATATTAAAT
1 -AATTTATTAT-TTAAAT
*
5236163 AATTTATTATTTTAAT
1 AATTTATTATTTAAAT
*
5236179 AAATTA-TATTTA
1 AATTTATTATTTA
5236191 TTATATTAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
15 9 0.19
16 19 0.40
17 14 0.30
18 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTATTATTTAAAT
Found at i:5236316 original size:18 final size:17
Alignment explanation
Indices: 5236257--5236316 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
5236247 TAATATTGAA
* *
5236257 AAATATAATATTTTAAT
1 AAATATAAAATTTTTAT
* *
5236274 AATTTTAAATATTTTTA-
1 AAATATAAA-ATTTTTAT
*
5236291 AAAAATAAAATTTATTAT
1 AAATATAAAATTT-TTAT
5236309 AAATATAA
1 AAATATAA
5236317 TAATAATAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
16 4 0.12
17 15 0.47
18 13 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATAAAATTTTTAT
Found at i:5236637 original size:2 final size:2
Alignment explanation
Indices: 5236626--5236688 Score: 64
Period size: 2 Copynumber: 34.0 Consensus size: 2
5236616 TAATACAGAA
*
5236626 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5236665 AT A- AC AG A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5236689 GTACACACAT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
1 5 0.09
2 49 0.91
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5242668 original size:17 final size:17
Alignment explanation
Indices: 5242646--5242680 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5242636 GATAATACTC
*
5242646 TAAAACGACATATTTTA
1 TAAAACGACAAATTTTA
5242663 TAAAACGACAAATTTTA
1 TAAAACGACAAATTTTA
5242680 T
1 T
5242681 GTGCTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (17 bp):
TAAAACGACAAATTTTA
Found at i:5242946 original size:12 final size:13
Alignment explanation
Indices: 5242929--5242957 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5242919 TGTTTAATTA
5242929 TATTA-GGATAAT
1 TATTAGGGATAAT
5242941 TATTAGGGATAAT
1 TATTAGGGATAAT
5242954 TATT
1 TATT
5242958 TAGATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (13 bp):
TATTAGGGATAAT
Found at i:5243003 original size:10 final size:10
Alignment explanation
Indices: 5242974--5243023 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
5242964 TAATTTTAGG
5242974 ATTTAT-TTT
1 ATTTATCTTT
*
5242983 CATTCATCTTT
1 -ATTTATCTTT
*
5242994 AATTATCTTT
1 ATTTATCTTT
5243004 ATTTAT-TTGT
1 ATTTATCTT-T
5243014 ATTTATCTTT
1 ATTTATCTTT
5243024 TAGAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 2 0.06
10 26 0.79
11 5 0.15
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:5243562 original size:19 final size:19
Alignment explanation
Indices: 5243537--5243716 Score: 261
Period size: 19 Copynumber: 9.9 Consensus size: 19
5243527 ATAATCTTCA
5243537 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
5243556 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5243575 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5243592 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
5243610 ATGATA--CAATATTAGAT
1 ATGATATGCAATCTTAGAT
5243627 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5243645 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5243662 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
5243680 ATGATATACAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
5243699 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
5243717 AGATATGATT
Statistics
Matches: 147, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
17 47 0.32
18 47 0.32
19 53 0.36
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5243607 original size:35 final size:35
Alignment explanation
Indices: 5243545--5243716 Score: 281
Period size: 35 Copynumber: 4.8 Consensus size: 35
5243535 CAATGATATG
*
5243545 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
5243581 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
*
5243616 CAATATTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
5243651 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
*
5243688 CAATCTTAGATATGATATACAATCTTAGA
1 CAATCTTAGATATGAT-TGCAATCTTAGA
5243717 AGATATGATT
Statistics
Matches: 129, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
35 84 0.65
36 15 0.12
37 19 0.15
38 11 0.09
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:5244279 original size:26 final size:25
Alignment explanation
Indices: 5244232--5244280 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5244222 TTATAAATAT
* * *
5244232 ATTTTTATTATATATTATATTTTAA
1 ATTTTTATTAAATATCACATTTTAA
5244257 ATTTATTATTAAATATCACATTTT
1 ATTT-TTATTAAATATCACATTTT
5244281 TTTATATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTTATTAAATATCACATTTTAA
Found at i:5249822 original size:8 final size:8
Alignment explanation
Indices: 5249808--5249870 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
5249798 CTATTTCAAA
5249808 AAAAAAAGG
1 AAAAAAA-G
5249817 AAAAAAAG
1 AAAAAAAG
5249825 AAAAGAAA-
1 AAAA-AAAG
5249833 AAAAAAA-
1 AAAAAAAG
5249840 AAGAAAAA-
1 AA-AAAAAG
*
5249848 TAAAAAAG
1 AAAAAAAG
*
5249856 AGATAAAAG
1 A-AAAAAAG
5249865 AAAAAA
1 AAAAAA
5249871 TGGAGAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
7 10 0.22
8 19 0.41
9 17 0.37
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5249823 original size:13 final size:13
Alignment explanation
Indices: 5249805--5249870 Score: 71
Period size: 13 Copynumber: 4.8 Consensus size: 13
5249795 CTTCTATTTC
5249805 AAAAAAAAAAGGA
1 AAAAAAAAAAGGA
5249818 AAAAAAGAAAA-GA
1 AAAAAA-AAAAGGA
*
5249831 AAAAAAAAAAAGA
1 AAAAAAAAAAGGA
5249844 AAAATAAAAAAGAGA
1 AAAA-AAAAAAG-GA
5249859 TAAAAGAAAAAA
1 -AAAA-AAAAAA
5249871 TGGAGAGGCC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
12 4 0.09
13 20 0.43
14 10 0.22
15 2 0.04
16 10 0.22
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAGGA
Found at i:5249838 original size:18 final size:18
Alignment explanation
Indices: 5249817--5249870 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
5249807 AAAAAAAAGG
5249817 AAAAAAAGAAAAGAAAAA
1 AAAAAAAGAAAAGAAAAA
*
5249835 AAAAAAAGAAAA-ATAAA
1 AAAAAAAGAAAAGAAAAA
* * *
5249852 AAAGAGATAAAAGAAAAA
1 AAAAAAAGAAAAGAAAAA
5249870 A
1 A
5249871 TGGAGAGGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (18 bp):
AAAAAAAGAAAAGAAAAA
Found at i:5249840 original size:26 final size:26
Alignment explanation
Indices: 5249805--5249870 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 26
5249795 CTTCTATTTC
*
5249805 AAAAAAAAAAGGAAAAA-AAGAAAAGA
1 AAAAAAAAAAAGAAAAATAA-AAAAGA
5249831 AAAAAAAAAAAGAAAAATAAAAAAGA
1 AAAAAAAAAAAGAAAAATAAAAAAGA
5249857 GATAAAAGAAAAAA
1 -A-AAAA-AAAAAA
5249871 TGGAGAGGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 22 0.63
27 3 0.09
28 4 0.11
29 6 0.17
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (26 bp):
AAAAAAAAAAAGAAAAATAAAAAAGA
Found at i:5250822 original size:44 final size:44
Alignment explanation
Indices: 5250770--5251293 Score: 358
Period size: 44 Copynumber: 11.9 Consensus size: 44
5250760 TAAAATTTGG
*
5250770 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAAATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * ** *
5250814 CATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG--CATGG
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
** * *
5250858 CATCCCTGTGTTTATAGGGAACA-AGTTAAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
* *
5250902 CATCCCTGTGTTTATAGGGAATAGATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * ** * * ** *
5250946 CA-CTTCTGTGCTTACAGCTAAGCAGATTGAGGATTTCAG--CATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * *
5250990 CATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
*
5251034 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * **
5251078 CA-CTCCTGTGCTTACAGCGAAGCAGATCGAGGATTTCAG--CATGA
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * * *
5251122 CATCCTTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
*
5251166 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * * ** *
5251210 CA-CTCCTATGCTTACAGCGAAGCAGATTGAAGATTTCAG--CATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * *
5251254 TATCCCTGTGTTTATAGGGAACA-AGTTGAAGACAGCAGAT
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGAT
5251294 TCGGCATCTC
Statistics
Matches: 367, Mismatches: 84, Indels: 57
0.72 0.17 0.11
Matches are distributed among these distances:
42 4 0.01
43 53 0.14
44 250 0.68
45 60 0.16
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
Found at i:5250990 original size:132 final size:132
Alignment explanation
Indices: 5250764--5251337 Score: 925
Period size: 132 Copynumber: 4.3 Consensus size: 132
5250754 AAGAAATAAA
* * *
5250764 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAAATCTGACATTCCTGTGCTTAC
1 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTTAC
*
5250829 AGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTAAAGATAGC
66 AGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
5250894 AG
131 AG
* *
5250896 ATTTGGCATCCCTGTGTTTATAGGGAATAGATCGAAGATAACAGATCTGACACTTCTGTGCTTAC
1 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTTAC
* * *
5250961 AGCTAAGCAGATTGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
66 AGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
5251026 AG
131 AG
5251028 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTTAC
1 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTTAC
* * *
5251093 AGCGAAGCAGATCGAGGATTTCAGCATGACATCCTTGTGTTTATAGGGAACAAGTTGAAGATAGC
66 AGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
5251158 AG
131 AG
*
5251160 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTATGCTTAC
1 ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTTAC
* * *
5251225 AGCGAAGCAGATTGAAGATTTCAGCATGGTATCCCTGTGTTTATAGGGAACAAGTTGAAGACAGC
66 AGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
5251290 AG
131 AG
* * * * * * *
5251292 ATTCGGCATCTCTGTATTGT-CAGAGAGCAGATCGAAGATACCAGAT
1 ATTTGGCATCCCTGTGTT-TATAGGGAACAGATCGAAGATAACAGAT
5251338 TTGGCATCTC
Statistics
Matches: 412, Mismatches: 29, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
132 411 1.00
133 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
ATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTTAC
AGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
AG
Found at i:5251344 original size:44 final size:44
Alignment explanation
Indices: 5251289--5251373 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
5251279 TTGAAGACAG
*
5251289 CAGATTCGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAC
1 CAGATTCGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAC
*
5251333 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGA
1 CAGATTCGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGA
5251374 CATAGCTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (44 bp):
CAGATTCGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAC
Found at i:5251722 original size:205 final size:205
Alignment explanation
Indices: 5251370--5251869 Score: 820
Period size: 205 Copynumber: 2.4 Consensus size: 205
5251360 GAGCAGATCG
5251370 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTC
1 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTC
*
5251435 TGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCTACTTCAATAGAGAGCAGATACATAGCAG
66 TGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAATAGAGAGCAGATACATAGCAG
*
5251500 ATCTCACCTTCAGATGTTTATGCTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAG
131 ATCTCACCTTCAGATGTTTATGCTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAG
5251565 GAACAAATCA
196 GAACAAATCA
* *
5251575 AAGACATAGCTGATTTGGCTTTCACGTATTTACGATGAAGCAAATCTAAGATGATTTGTCGTCTC
1 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTC
* * * * * * * * *
5251640 TGTAGTGTCAGAGAACAAATTGAAGTTTGGCATTTCCACTTTAATGGAGAGCGGATACATGGTAG
66 TGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAATAGAGAGCAGATACATAGCAG
5251705 ATCTCACCTTCAGATGTTTATGCTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAG
131 ATCTCACCTTCAGATGTTTATGCTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAG
* *
5251770 GAGCAAATCG
196 GAACAAATCA
* * * *
5251780 AAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCAAATCTAAGATGATTTGGCATCTC
1 AAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTC
*
5251845 TGTATTGTCAGGGAACAAATCGAAG
66 TGTATTGTCAGAGAACAAATCGAAG
5251870 AAGTTAATTT
Statistics
Matches: 271, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
205 271 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (205 bp):
AAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTC
TGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCAATAGAGAGCAGATACATAGCAG
ATCTCACCTTCAGATGTTTATGCTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAG
GAACAAATCA
Found at i:5252282 original size:18 final size:18
Alignment explanation
Indices: 5252234--5252360 Score: 193
Period size: 18 Copynumber: 6.9 Consensus size: 18
5252224 ATAATCTTCA
5252234 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
5252253 GTGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
5252272 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
5252290 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
5252307 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
5252325 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
5252343 ATGATATACAATCTTAGA
1 ATGAT-TGCAATCTTAGA
5252361 AGATATGATT
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
17 16 0.16
18 52 0.51
19 33 0.33
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:5252307 original size:35 final size:36
Alignment explanation
Indices: 5252234--5252360 Score: 186
Period size: 35 Copynumber: 3.5 Consensus size: 36
5252224 ATAATCTTCA
*
5252234 ATGATATGCAATCTTAGATGTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATA--CAATCTTAGAT
5252272 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
*
5252307 ATGAT-TGCAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGA-TACAATCTTAGAT
*
5252343 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
5252361 AGATATGATT
Statistics
Matches: 84, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
35 33 0.39
36 17 0.20
37 29 0.35
38 5 0.06
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (36 bp):
ATGATATGCAATCTTAGATATGATACAATCTTAGAT
Found at i:5252328 original size:53 final size:55
Alignment explanation
Indices: 5252242--5252367 Score: 206
Period size: 53 Copynumber: 2.3 Consensus size: 55
5252232 CAATGATATG
*
5252242 CAATCTTAGATGTGATATGCAATCTTAGATATGATTGCAATCTTAGATATG-ATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATTGCAATCTTAGATATGAATA
5252296 CAATCTTAGATATGAT-TGCAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATTGCAATCTTAGATATGA-ATA
5252351 CAATCTTAGA-A-GATATG
1 CAATCTTAGATATGATATG
5252368 ATTTTGTAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
53 37 0.54
54 18 0.26
55 13 0.19
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (55 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGATTGCAATCTTAGATATGAATA
Found at i:5252903 original size:17 final size:17
Alignment explanation
Indices: 5252838--5252903 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
5252828 TCTAACCCAA
*
5252838 TATATTTTATATTTT-T
1 TATATATTATATTTTAT
5252854 TATATAATTATTATTCTTA-
1 TATAT-ATTA-TATT-TTAT
*
5252873 TAAATA-TAT-TTTTAT
1 TATATATTATATTTTAT
5252888 TATATATTATATTTTA
1 TATATATTATATTTTA
5252904 AATTTATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
14 3 0.08
15 7 0.17
16 9 0.22
17 10 0.25
18 5 0.12
19 6 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATATTATATTTTAT
Found at i:5252927 original size:26 final size:25
Alignment explanation
Indices: 5252880--5252928 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5252870 TTATAAATAT
* * *
5252880 ATTTTTATTATATATTATATTTTAA
1 ATTTTTATTAAATATCACATTTTAA
5252905 ATTTATTATTAAATATCACATTTT
1 ATTT-TTATTAAATATCACATTTT
5252929 TTTATATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTTATTAAATATCACATTTTAA
Found at i:5261151 original size:24 final size:26
Alignment explanation
Indices: 5261121--5261169 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
5261111 AATTTAAAAA
5261121 TATTTAAAA-AATAAAAAAA-ATAAT
1 TATTTAAAACAATAAAAAAATATAAT
*
5261145 TATTTAAAACTATAAAAAAATATAA
1 TATTTAAAACAATAAAAAAATATAA
5261170 ACTTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
25 9 0.41
26 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
TATTTAAAACAATAAAAAAATATAAT
Found at i:5261614 original size:12 final size:12
Alignment explanation
Indices: 5261597--5261626 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5261587 CTAAATGTCG
5261597 TTATATATTTTT
1 TTATATATTTTT
5261609 TTATATATTTTT
1 TTATATATTTTT
5261621 TTATAT
1 TTATAT
5261627 TCTTTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATATATTTTT
Found at i:5261678 original size:35 final size:35
Alignment explanation
Indices: 5261628--5261701 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
5261618 TTTTTATATT
* *
5261628 CTTTAAATGTTTATGTAAGTTATGATAATCATTAA
1 CTTTAAATGTCTATGTAAATTATGATAATCATTAA
5261663 CTTTAAATGTCTATGTAAATTATGATAATCATTAA
1 CTTTAAATGTCTATGTAAATTATGATAATCATTAA
5261698 CTTT
1 CTTT
5261702 TATTTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.46
Consensus pattern (35 bp):
CTTTAAATGTCTATGTAAATTATGATAATCATTAA
Found at i:5264020 original size:64 final size:64
Alignment explanation
Indices: 5263810--5264020 Score: 142
Period size: 64 Copynumber: 3.2 Consensus size: 64
5263800 CTGGGCCAGA
* *
5263810 GCCCTTTTCAGATCACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
5263874 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
5263936 ACTGGGCCA-AA
54 A-TGGCCCATAG
*
5263947 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
5264011 GCCCATTTCA
1 GCCCATTTCA
5264021 AAATACATGC
Statistics
Matches: 102, Mismatches: 28, Indels: 34
0.62 0.17 0.21
Matches are distributed among these distances:
63 8 0.08
64 25 0.25
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 17 0.17
74 8 0.08
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:5264022 original size:137 final size:136
Alignment explanation
Indices: 5263776--5264061 Score: 518
Period size: 137 Copynumber: 2.1 Consensus size: 136
5263766 CTATTGGCCT
** *
5263776 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATCACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATCACAATAAACTGGGCCTT
*
5263841 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
5263906 CATATGC
130 CATATGC
*
5263913 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATCACAATAAACTGGGCCTT
5263978 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
5264043 ATATGC
131 ATATGC
5264049 AAGCCCATTTGGG
1 AAGCCCATTTGGG
5264062 GAGACTACTC
Statistics
Matches: 144, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
136 22 0.15
137 122 0.85
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATCACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:5265883 original size:26 final size:26
Alignment explanation
Indices: 5265847--5265982 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5265837 CATGATATTC
*
5265847 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
5265873 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
5265899 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
5265925 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5265951 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5265977 TTATCA
1 TTATCA
5265983 ATTTGTATCA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 107 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5272156 original size:22 final size:22
Alignment explanation
Indices: 5272128--5272182 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
5272118 CTTCTATTAT
5272128 TATGTATGTACCTTAATACATA
1 TATGTATGTACCTTAATACATA
5272150 TATGTATGTACCTTAATACATA
1 TATGTATGTACCTTAATACATA
5272172 TATGTATGTAC
1 TATGTATGTAC
5272183 TACTGTCGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGTATGTACCTTAATACATA
Found at i:5272957 original size:13 final size:13
Alignment explanation
Indices: 5272936--5272965 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5272926 TATTTTAATT
*
5272936 ATTTTCTAATAAA
1 ATTTCCTAATAAA
5272949 ATTTCCTAATAAA
1 ATTTCCTAATAAA
5272962 ATTT
1 ATTT
5272966 TTGCCTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTCCTAATAAA
Found at i:5273893 original size:17 final size:18
Alignment explanation
Indices: 5273873--5273906 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5273863 AAGTGAATTG
5273873 AAATTGC-GAAATTAAAT
1 AAATTGCAGAAATTAAAT
5273890 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
5273907 ATGAGGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:5279121 original size:15 final size:15
Alignment explanation
Indices: 5279101--5279165 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
5279091 GTATCTTGGG
5279101 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
5279116 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
5279131 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
5279146 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
5279160 TTTCTT
1 TTTCTT
5279166 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
14 10 0.23
15 31 0.72
16 2 0.05
ACGTcount: A:0.09, C:0.15, G:0.14, T:0.62
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:5279132 original size:30 final size:30
Alignment explanation
Indices: 5279097--5279165 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
5279087 TATTGTATCT
5279097 TGGGTTTCTTTAT-TCTGGATTTCTTTATTC
1 TGGGTTTCTTTATCT-TGGATTTCTTTATTC
*
5279127 TGGGTTTCTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTTTATCTTGGATTTCTTTATTC
*
5279157 -GGTTTTCTT
1 TGGGTTTCTT
5279166 GTTATCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 7 0.20
30 27 0.77
31 1 0.03
ACGTcount: A:0.09, C:0.14, G:0.17, T:0.59
Consensus pattern (30 bp):
TGGGTTTCTTTATCTTGGATTTCTTTATTC
Found at i:5288284 original size:45 final size:46
Alignment explanation
Indices: 5288235--5288322 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
5288225 CATTTAAGCA
5288235 TTTAGATCAAAAGCCAGA-AAAACAAATTTATATATTTTTCTTAAT
1 TTTAGATCAAAAGCCAGAGAAAACAAATTTATATATTTTTCTTAAT
** * *
5288280 TTTAGATCAAAAGCTTGAGAAAAGAAGTTTATATATTTTTCTT
1 TTTAGATCAAAAGCCAGAGAAAACAAATTTATATATTTTTCTT
5288323 GAAGAGTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 16 0.42
46 22 0.58
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (46 bp):
TTTAGATCAAAAGCCAGAGAAAACAAATTTATATATTTTTCTTAAT
Found at i:5291690 original size:43 final size:43
Alignment explanation
Indices: 5291642--5291726 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
5291632 AAGGTTATAA
5291642 CCTTTAGCAACGCTTTTAC-CACAAACGCCGCTAAAGGTCATGG
1 CCTTTAGCAACGCTTTT-CGCACAAACGCCGCTAAAGGTCATGG
** *
5291685 CCTTTAGCGGCGCTTTTCGCACAAACGCCGCTAAAGTTCATG
1 CCTTTAGCAACGCTTTTCGCACAAACGCCGCTAAAGGTCATG
5291727 AAATTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (43 bp):
CCTTTAGCAACGCTTTTCGCACAAACGCCGCTAAAGGTCATGG
Found at i:5291905 original size:19 final size:19
Alignment explanation
Indices: 5291860--5291906 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5291850 ATCAAATTAA
*
5291860 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
5291879 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
5291898 AATAAAAAT
1 AATAAAAAT
5291907 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:5294839 original size:3 final size:3
Alignment explanation
Indices: 5294571--5294824 Score: 112
Period size: 3 Copynumber: 83.7 Consensus size: 3
5294561 AAAAAAGAAG
* * * * *
5294571 TAA TGA TAA TAA TAA TAG GAG TAA TAA TAA T-A TAA TGA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* * * * * *
5294616 CAA TAA TAA -AA GGAA CAA AAA TAA TAG TAA TAA -AA -AA TATT TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * *
5294660 TAA TAG TAA TAA TAA CAA TAA T-A TAAA TAA TAA TATA TACA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA-A TA-A TAA TAA
* * *
5294707 TAA TAA TAGT TAGA -AA TAA -AA -AA TAA TGGAA GTAG TAA TAA CAA
1 TAA TAA TA-A TA-A TAA TAA TAA TAA TAA T--AA -TAA TAA TAA TAA
** * * * * * *
5294751 TGG TAA TAG TAA TAA -AGA TAA CAG TAA GAA AAA TAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
5294796 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5294825 TATCGAAAAT
Statistics
Matches: 189, Mismatches: 45, Indels: 34
0.71 0.17 0.13
Matches are distributed among these distances:
2 16 0.08
3 151 0.80
4 19 0.10
5 2 0.01
6 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:5297957 original size:18 final size:18
Alignment explanation
Indices: 5297934--5297986 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
5297924 CGTTTACAAT
5297934 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
*
5297952 ACTATTCCCGTATACGGC
1 ACTATTCACGTATACGGC
5297970 ACTATTCACGTATACGG
1 ACTATTCACGTATACGG
5297987 TAGTTGGGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:5305549 original size:21 final size:21
Alignment explanation
Indices: 5305525--5305586 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
5305515 CATAAATACT
*
5305525 AAACCCTTAACCCTTAACCCC
1 AAACCCTTAACCCTTAAACCC
*
5305546 AAACCCTT-ACACCTTAAACTC
1 AAACCCTTAAC-CCTTAAACCC
*
5305567 TAACCC-TAACCCTTAAACCC
1 AAACCCTTAACCCTTAAACCC
5305587 TAAATCATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 12 0.34
21 23 0.66
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACCCTTAACCCTTAAACCC
Found at i:5305587 original size:14 final size:14
Alignment explanation
Indices: 5305524--5305589 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
5305514 CCATAAATAC
5305524 TAAACCCTTAACCCT
1 TAAACCC-TAACCCT
* *
5305539 TAACCCCAAACCCT
1 TAAACCCTAACCCT
* * *
5305553 TACACCTTAA-ACT
1 TAAACCCTAACCCT
5305566 CT-AACCCTAACCCT
1 -TAAACCCTAACCCT
5305580 TAAACCCTAA
1 TAAACCCTAA
5305590 ATCATAATCC
Statistics
Matches: 38, Mismatches: 10, Indels: 7
0.69 0.18 0.13
Matches are distributed among these distances:
13 9 0.24
14 23 0.61
15 6 0.16
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAACCCT
Found at i:5305602 original size:27 final size:27
Alignment explanation
Indices: 5305524--5305590 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
5305514 CCATAAATAC
* * *
5305524 TAAACCCTTAACCCTTAACCCCAAACCCT
1 TAAACCCTAAACTC-TAA-CCCTAACCCT
* *
5305553 TACACCTTAAACTCTAACCCTAACCCT
1 TAAACCCTAAACTCTAACCCTAACCCT
5305580 TAAACCCTAAA
1 TAAACCCTAAA
5305591 TCATAATCCT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
27 18 0.58
28 3 0.10
29 10 0.32
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.22
Consensus pattern (27 bp):
TAAACCCTAAACTCTAACCCTAACCCT
Found at i:5305675 original size:21 final size:21
Alignment explanation
Indices: 5305644--5305735 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 21
5305634 AGTTAACTCC
* *
5305644 TAAACCTTAAACCCTAAACCA
1 TAAATCTTAAACCATAAACCA
* * *
5305665 TACATCTTAAACTATTGTTAACTCA
1 TAAATCTTAAACCA---TAAAC-CA
* *
5305690 TAAACCTTAAACCTTAAACCA
1 TAAATCTTAAACCATAAACCA
* *
5305711 TATATCTTAAACCATAAACCT
1 TAAATCTTAAACCATAAACCA
5305732 TAAA
1 TAAA
5305736 CTATAATGAT
Statistics
Matches: 52, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
21 32 0.62
22 4 0.08
24 4 0.08
25 12 0.23
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.29
Consensus pattern (21 bp):
TAAATCTTAAACCATAAACCA
Found at i:5305702 original size:7 final size:7
Alignment explanation
Indices: 5305690--5305736 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
5305680 TGTTAACTCA
5305690 TAAACCT
1 TAAACCT
5305697 TAAACCT
1 TAAACCT
*
5305704 TAAACCA
1 TAAACCT
* *
5305711 TATATCT
1 TAAACCT
*
5305718 TAAACCA
1 TAAACCT
5305725 TAAACCT
1 TAAACCT
5305732 TAAAC
1 TAAAC
5305737 TATAATGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAACCT
Found at i:5305702 original size:46 final size:46
Alignment explanation
Indices: 5305635--5305722 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
5305625 TCAAATACTA
*
5305635 GTTAACTCCTAAACCTTAAACCCTAAACCATACATCTTAAACTATT
1 GTTAACTCATAAACCTTAAACCCTAAACCATACATCTTAAACTATT
* *
5305681 GTTAACTCATAAACCTTAAACCTTAAACCATATATCTTAAAC
1 GTTAACTCATAAACCTTAAACCCTAAACCATACATCTTAAAC
5305723 CATAAACCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.31
Consensus pattern (46 bp):
GTTAACTCATAAACCTTAAACCCTAAACCATACATCTTAAACTATT
Found at i:5305707 original size:14 final size:14
Alignment explanation
Indices: 5305690--5305797 Score: 83
Period size: 14 Copynumber: 7.7 Consensus size: 14
5305680 TGTTAACTCA
*
5305690 TAAACCTTAAACCT
1 TAAACCATAAACCT
* *
5305704 TAAACCATATATCT
1 TAAACCATAAACCT
5305718 TAAACCATAAACCT
1 TAAACCATAAACCT
* ***
5305732 TAAACTAT-AATGA
1 TAAACCATAAACCT
***
5305745 TAATTAATTAAACCT
1 TAAACCA-TAAACCT
* *
5305760 TAAACCATATATCT
1 TAAACCATAAACCT
5305774 TAAACCATAAACCT
1 TAAACCATAAACCT
*
5305788 TAAACTATAA
1 TAAACCATAA
5305798 TGATAATTAA
Statistics
Matches: 69, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
13 6 0.09
14 57 0.83
15 6 0.09
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:5305730 original size:28 final size:28
Alignment explanation
Indices: 5305690--5305792 Score: 127
Period size: 28 Copynumber: 3.7 Consensus size: 28
5305680 TGTTAACTCA
*
5305690 TAAACCTTAAACCTTAAACCATATATCT
1 TAAACCATAAACCTTAAACCATATATCT
* **
5305718 TAAACCATAAACCTTAAACTATA-ATGA
1 TAAACCATAAACCTTAAACCATATATCT
***
5305745 TAATTAATTAAACCTTAAACCATATATCT
1 TAAACCA-TAAACCTTAAACCATATATCT
5305774 TAAACCATAAACCTTAAAC
1 TAAACCATAAACCTTAAAC
5305793 TATAATGATA
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
27 6 0.10
28 48 0.80
29 6 0.10
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.30
Consensus pattern (28 bp):
TAAACCATAAACCTTAAACCATATATCT
Found at i:5305770 original size:56 final size:56
Alignment explanation
Indices: 5305696--5305809 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
5305686 CTCATAAACC
5305696 TTAAACCTTAAACCATATATCTTAAACCATAAACCTTAAACTATAATGATAATTAA
1 TTAAACCTTAAACCATATATCTTAAACCATAAACCTTAAACTATAATGATAATTAA
5305752 TTAAACCTTAAACCATATATCTTAAACCATAAACCTTAAACTATAATGATAATTAA
1 TTAAACCTTAAACCATATATCTTAAACCATAAACCTTAAACTATAATGATAATTAA
5305808 TT
1 TT
5305810 CAATATTTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (56 bp):
TTAAACCTTAAACCATATATCTTAAACCATAAACCTTAAACTATAATGATAATTAA
Found at i:5306011 original size:41 final size:41
Alignment explanation
Indices: 5305954--5306122 Score: 250
Period size: 41 Copynumber: 4.1 Consensus size: 41
5305944 GTTATATGAC
5305954 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
*
5305995 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
* * * *
5306036 TTTTAGTGGCGTTTCAACAAAAGCACCGCTAATGCTCTAGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
* * *
5306077 TTTTAGCGGCGTTTTACCAAAAACGCCACTATTGCTCT-GT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
5306117 GTTTTA
1 -TTTTA
5306123 CAATTTTTGC
Statistics
Matches: 114, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 2 0.02
41 112 0.98
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
Found at i:5307137 original size:23 final size:23
Alignment explanation
Indices: 5307107--5307150 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5307097 CCTAGGGAGA
5307107 TGAACCCTATGATAGATTCTAGG
1 TGAACCCTATGATAGATTCTAGG
*
5307130 TGAACCCTATGATGGATTCTA
1 TGAACCCTATGATAGATTCTA
5307151 TCTTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (23 bp):
TGAACCCTATGATAGATTCTAGG
Found at i:5310515 original size:144 final size:144
Alignment explanation
Indices: 5310245--5310741 Score: 603
Period size: 144 Copynumber: 3.5 Consensus size: 144
5310235 GCATTGGTAG
* * * * * *
5310245 TTTATCAAATTTAACTTCATTAGAGCTC-CACCAAAATAAATTGAATGGTTCAATCCCTTCTTGT
1 TTTAGCAAATTTAACTTCATTAGACCTCTC-CCAAAACAATTTAAATGGTCCAATCCCTTCTTGT
* * * *
5310309 CTTGGTAGTTTATCAAAGATGCAGTACTTGAGCCTTAGTTTTAATCTATTCAAAGGTCCTATTCC
65 ATTGGTAGTTTATCAAAGATGCAGTACTTGAGCCTTGGTTCTAATCTATTAAAAGGTCCTATTCC
*
5310374 CCAAGGACTTTGTAA
130 CCAAGAACTTTGTAA
*
5310389 TTTAGCAAATTTAACTTTATTAGACCTCTCCCAAAACAATTTAAATGGTCCAATCCCTTCTTGTA
1 TTTAGCAAATTTAACTTCATTAGACCTCTCCCAAAACAATTTAAATGGTCCAATCCCTTCTTGTA
* * *
5310454 TTGGTAGTTTATCAAAAATGCAGTACTT-AGGCTTTGGTTCTAATCTATTAAAAGGTTCTATTCC
66 TTGGTAGTTTATCAAAGATGCAGTACTTGA-GCCTTGGTTCTAATCTATTAAAAGGTCCTATTCC
5310518 CCAAGAACTTTGTAA
130 CCAAGAACTTTGTAA
* * * * *
5310533 TTTAGTAAATTTAACTTTATTACACGTCTCCCAAAACAATTTAAGTGGTCCAAT-CCTTCTTGTA
1 TTTAGCAAATTTAACTTCATTAGACCTCTCCCAAAACAATTTAAATGGTCCAATCCCTTCTTGTA
* * ** * *
5310597 TTGGTAATTAATTGAAGCTGC-GGATCTTGAGCCTTGGTTCTAATCTATTAAAAGGTCCTATTCC
66 TTGGTAGTTTATCAAAGATGCAGTA-CTTGAGCCTTGGTTCTAATCTATTAAAAGGTCCTATTCC
* *
5310661 CTAAGAAATTTGTAA
130 CCAAGAACTTTGTAA
* * * * * *
5310676 TTTAGAAAATTTAACTTCATT-GTACCTCTCCCAAAA-AA-TTGAGTGATGCAATCCCATCTTGT
1 TTTAGCAAATTTAACTTCATTAG-ACCTCTCCCAAAACAATTTAAATGGTCCAATCCCTTCTTGT
5310738 ATTG
65 ATTG
5310742 ACAATTTATC
Statistics
Matches: 309, Mismatches: 38, Indels: 14
0.86 0.11 0.04
Matches are distributed among these distances:
141 11 0.04
142 16 0.05
143 105 0.34
144 176 0.57
145 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (144 bp):
TTTAGCAAATTTAACTTCATTAGACCTCTCCCAAAACAATTTAAATGGTCCAATCCCTTCTTGTA
TTGGTAGTTTATCAAAGATGCAGTACTTGAGCCTTGGTTCTAATCTATTAAAAGGTCCTATTCCC
CAAGAACTTTGTAA
Found at i:5315296 original size:21 final size:20
Alignment explanation
Indices: 5315269--5315318 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
5315259 TAATAATGTG
* *
5315269 ATAGTAATGATAATAATAAT
1 ATAGTAATAATAAGAATAAT
*
5315289 AGTAGTAAAAATAAGAATAAT
1 A-TAGTAATAATAAGAATAAT
5315310 ATAGTAATA
1 ATAGTAATA
5315319 GTGTTAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (20 bp):
ATAGTAATAATAAGAATAAT
Found at i:5315548 original size:13 final size:13
Alignment explanation
Indices: 5315516--5315550 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5315506 GCAATAATAG
5315516 CAATAATAATAAA
1 CAATAATAATAAA
* *
5315529 TATTAATAATAAA
1 CAATAATAATAAA
5315542 CAATAATAA
1 CAATAATAA
5315551 AAGGAATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (13 bp):
CAATAATAATAAA
Found at i:5315803 original size:3 final size:3
Alignment explanation
Indices: 5315788--5315849 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
5315778 TAATTTCAAA
*
5315788 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5315836 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
5315850 ATATAGAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5316097 original size:3 final size:3
Alignment explanation
Indices: 5316053--5316085 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5316043 AATAGTGGTG
5316053 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5316086 CAAACAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5316157 original size:15 final size:15
Alignment explanation
Indices: 5316137--5316170 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5316127 AGAAATAAAA
5316137 AATAATAGA-AGTAAT
1 AATAAT-GATAGTAAT
5316152 AATAATGATAGTAAT
1 AATAATGATAGTAAT
5316167 AATA
1 AATA
5316171 TAAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (15 bp):
AATAATGATAGTAAT
Found at i:5316217 original size:12 final size:13
Alignment explanation
Indices: 5316200--5316256 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 13
5316190 TATATATGAT
5316200 ATAATAATATA-A
1 ATAATAATATATA
5316212 ATAATAATATATA
1 ATAATAATATATA
5316225 TATGAGA-AATA-ATA
1 -AT-A-ATAATATATA
5316239 ATAATAATATA-A
1 ATAATAATATATA
5316251 ATAATA
1 ATAATA
5316257 GCAAAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
11 1 0.03
12 23 0.59
13 4 0.10
14 5 0.13
15 5 0.13
16 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (13 bp):
ATAATAATATATA
Found at i:5316236 original size:21 final size:18
Alignment explanation
Indices: 5316200--5316256 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
5316190 TATATATGAT
*
5316200 ATAATAATATAAATAATA
1 ATAATAATAGAAATAATA
5316218 ATATATATATGAGAAATAATA
1 ATA-ATA-AT-AGAAATAATA
*
5316239 ATAATAATATAAATAATA
1 ATAATAATAGAAATAATA
5316257 GCAAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
ATAATAATAGAAATAATA
Done.