Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008541.1 Kokia drynarioides strain JFW-HI SEQ_123218, whole genome shotgun sequence
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: 99072
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:2461 original size:51 final size:51
Alignment explanation
Indices: 2381--2483 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
2371 TGCTCATTTT
* *
2381 TGTATAATTTTTCAAATAGTGGGGGTTGAAATTTGTAGAGAAAAAACGCTC
1 TGTATAAATTTTCAAATAGTGGGGATTGAAATTTGTAGAGAAAAAACGCTC
*
2432 TGTATAAATTTTCAAATAGTGGGGATTGAAATTTGTAGAGAAAAAACTCTC
1 TGTATAAATTTTCAAATAGTGGGGATTGAAATTTGTAGAGAAAAAACGCTC
2483 T
1 T
2484 AAGCAGGATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (51 bp):
TGTATAAATTTTCAAATAGTGGGGATTGAAATTTGTAGAGAAAAAACGCTC
Found at i:2810 original size:28 final size:28
Alignment explanation
Indices: 2770--2848 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
2760 ATTAATCTCT
*
2770 TCAAAATAATTTTTCAGAACACATC-AC
1 TCAAAATTATTTTTCAGAACACATCTAC
* * * *
2797 GTCAAATTTATTTTTCAAAACCCATCTTC
1 -TCAAAATTATTTTTCAGAACACATCTAC
2826 TCAAAATTATTTTTTCTAGAACA
1 TCAAAATTA-TTTTTC-AGAACA
2849 ATACTTAGCA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 29 0.73
29 7 0.17
30 4 0.10
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (28 bp):
TCAAAATTATTTTTCAGAACACATCTAC
Found at i:3139 original size:22 final size:22
Alignment explanation
Indices: 3102--3216 Score: 90
Period size: 22 Copynumber: 5.2 Consensus size: 22
3092 CAATTTTCCA
*
3102 AAACTCTTAATTTAAAATACCTT
1 AAACCCTT-ATTTAAAATACCTT
3125 AAACCCTTATTTAAAATACCTT
1 AAACCCTTATTTAAAATACCTT
* * * **
3147 AAATCCTAATTTAAAAAACCAA
1 AAACCCTTATTTAAAATACCTT
** *
3169 AAATTCTTATTTAAATTACAC--
1 AAACCCTTATTTAAAATAC-CTT
* * *
3190 AAACCCTAATTTAAAAAACCCT
1 AAACCCTTATTTAAAATACCTT
3212 AAACC
1 AAACC
3217 TAATTAAACC
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.01
21 14 0.19
22 51 0.69
23 8 0.11
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (22 bp):
AAACCCTTATTTAAAATACCTT
Found at i:3159 original size:44 final size:43
Alignment explanation
Indices: 3109--3216 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 43
3099 CCAAAACTCT
* * *
3109 TAATTTAAAATACCTTAAACCCTTATTTAAAATAC-CTTAAATCC
1 TAATTTAAAAAACCATAAACCCTTATTTAAAATACAC--AAACCC
* ** *
3153 TAATTTAAAAAACCAAAAATTCTTATTTAAATTACACAAACCC
1 TAATTTAAAAAACCATAAACCCTTATTTAAAATACACAAACCC
*
3196 TAATTTAAAAAACCCTAAACC
1 TAATTTAAAAAACCATAAACC
3217 TAATTAAACC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
43 22 0.42
44 29 0.56
45 1 0.02
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (43 bp):
TAATTTAAAAAACCATAAACCCTTATTTAAAATACACAAACCC
Found at i:3753 original size:23 final size:23
Alignment explanation
Indices: 3722--3769 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3712 TCTTGTTGCG
3722 TCATCGGGAC-AAAGATTTTCTTC
1 TCATCGGGACGAAA-ATTTTCTTC
*
3745 TCATTGGGACGAAAATTTTCTTC
1 TCATCGGGACGAAAATTTTCTTC
3768 TC
1 TC
3770 GCCGTGACGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (23 bp):
TCATCGGGACGAAAATTTTCTTC
Found at i:6977 original size:39 final size:39
Alignment explanation
Indices: 6857--6978 Score: 93
Period size: 39 Copynumber: 3.1 Consensus size: 39
6847 ATACTAATAA
** * * * * **
6857 TGACATTGTAAACACTATGATGCTATACTAAAATAACAG
1 TGACATTGTAAACACTGCGAAGCTATATTGAACTGGCAG
* * * *
6896 TGAGACTGTAAACTCTGCGAAGCTATATTGAACTGGTAG
1 TGACATTGTAAACACTGCGAAGCTATATTGAACTGGCAG
* * *
6935 TGACATTGTAAACACTGCGATGCTA-ATCTGATCTGGCGG
1 TGACATTGTAAACACTGCGAAGCTATAT-TGAACTGGCAG
6974 TGACA
1 TGACA
6979 CTATAAATGC
Statistics
Matches: 63, Mismatches: 19, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
38 2 0.03
39 61 0.97
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (39 bp):
TGACATTGTAAACACTGCGAAGCTATATTGAACTGGCAG
Found at i:8473 original size:21 final size:21
Alignment explanation
Indices: 8448--8491 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8438 ACTGAACGAG
8448 GTAGTACCGCTA-TTGGTAAAA
1 GTAGTACCG-TATTTGGTAAAA
*
8469 GTAGTACCGTATTTGGTAGAA
1 GTAGTACCGTATTTGGTAAAA
8490 GT
1 GT
8492 CGTAGGGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (21 bp):
GTAGTACCGTATTTGGTAAAA
Found at i:15768 original size:9 final size:9
Alignment explanation
Indices: 15705--15773 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
15695 AAATATAAAT
*
15705 TATAAAAAG
1 TATAAAAAA
*
15714 TACAAAAAA
1 TATAAAAAA
15723 -ATAAAAACA
1 TATAAAAA-A
15732 TGATAAAAAA
1 T-ATAAAAAA
*
15742 TAAAAAAAA
1 TATAAAAAA
* *
15751 TCTAGAAAA
1 TATAAAAAA
*
15760 TTTAAAAAA
1 TATAAAAAA
15769 TATAA
1 TATAA
15774 CACAATTATA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
8 6 0.13
9 32 0.68
10 2 0.04
11 7 0.15
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (9 bp):
TATAAAAAA
Found at i:15845 original size:10 final size:9
Alignment explanation
Indices: 15830--15906 Score: 63
Period size: 8 Copynumber: 8.6 Consensus size: 9
15820 AATTTATATT
15830 AAAATTATA
1 AAAATTATA
*
15839 GAAAATTAAAA
1 -AAAATT-ATA
15850 TAAAATTATCA
1 -AAAATTAT-A
15861 AAAATTAT-
1 AAAATTATA
15869 AAAA-TATA
1 AAAATTATA
*
15877 AAAAGTATA
1 AAAATTATA
*
15886 AAAA-AATA
1 AAAATTATA
15894 AAAATTA-A
1 AAAATTATA
15902 AAAAT
1 AAAAT
15907 AAAATGATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
7 3 0.05
8 21 0.37
9 9 0.16
10 15 0.26
11 9 0.16
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (9 bp):
AAAATTATA
Found at i:15889 original size:17 final size:16
Alignment explanation
Indices: 15849--15910 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
15839 GAAAATTAAA
*
15849 ATAAAATTATCAAAAAT
1 ATAAAAATAT-AAAAAT
15866 -TATAAAATATAAAAAGT
1 ATA-AAAATATAAAAA-T
*
15883 ATAAAAAAATAAAAAT
1 ATAAAAATATAAAAAT
15899 -TAAAAA-ATAAAA
1 ATAAAAATATAAAA
15911 TGATAAAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 6 0.15
15 6 0.15
16 8 0.20
17 18 0.45
18 2 0.05
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
ATAAAAATATAAAAAT
Found at i:20367 original size:20 final size:20
Alignment explanation
Indices: 20311--20435 Score: 85
Period size: 20 Copynumber: 6.2 Consensus size: 20
20301 ATAATGCTAT
*
20311 ACAGAGGCA-TCGTAGTGCAA
1 ACAGAGGCACT-GAAGTGCAA
* * *
20331 ATAGAGGCACCGGAGTGCAA
1 ACAGAGGCACTGAAGTGCAA
* * * *
20351 ATAGAGACATTGAAGTGTAA
1 ACAGAGGCACTGAAGTGCAA
*
20371 CCAGAGGCACTGAAGTGCAA
1 ACAGAGGCACTGAAGTGCAA
*
20391 ACAGAGGCAC-GACTGTGCAA
1 ACAGAGGCACTGA-AGTGCAA
* * *
20411 TCATAGGTACT-AGAGTGCAA
1 ACAGAGGCACTGA-AGTGCAA
20431 ACAGA
1 ACAGA
20436 AACACTGAAA
Statistics
Matches: 80, Mismatches: 22, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
19 2 0.03
20 78 0.98
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (20 bp):
ACAGAGGCACTGAAGTGCAA
Found at i:21123 original size:22 final size:23
Alignment explanation
Indices: 21081--21124 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21071 CCTTCAAATA
21081 CTAAAATTTACAGGATTTTCATG
1 CTAAAATTTACAGGATTTTCATG
* *
21104 CTAAACTTTACA-TATTTTCAT
1 CTAAAATTTACAGGATTTTCAT
21125 ATTAATCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (23 bp):
CTAAAATTTACAGGATTTTCATG
Found at i:24507 original size:15 final size:15
Alignment explanation
Indices: 24464--24508 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
24454 AATTTATAAA
24464 TTTTAAAATAAAAAT
1 TTTTAAAATAAAAAT
* **
24479 ATGAAAAATAAAAACT
1 TTTTAAAATAAAAA-T
24495 TTTTAAAATAAAAA
1 TTTTAAAATAAAAA
24509 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
TTTTAAAATAAAAAT
Found at i:24771 original size:43 final size:44
Alignment explanation
Indices: 24723--24809 Score: 131
Period size: 46 Copynumber: 2.0 Consensus size: 44
24713 GGGTATGGGC
*
24723 CAAATTGAC-AAAAAAATTATTAATGATGAGGGCTAAAAAAGGT
1 CAAATTGACAAAAAAAATTATTAATGATGAGGACTAAAAAAGGT
*
24766 CAAATTGACAAAAAAAAAATTATTAATGTTGAGGACTAAAAAAG
1 CAAATTGAC--AAAAAAAATTATTAATGATGAGGACTAAAAAAG
24810 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 9 0.23
46 30 0.77
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.23
Consensus pattern (44 bp):
CAAATTGACAAAAAAAATTATTAATGATGAGGACTAAAAAAGGT
Found at i:26660 original size:45 final size:45
Alignment explanation
Indices: 26610--26705 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
26600 TGTGTTCCTT
*
26610 TAGATGAGTTCATTCTTTGTATTTATATAATATGGTCACTGTCCA
1 TAGATGAGTTAATTCTTTGTATTTATATAATATGGTCACTGTCCA
** *
26655 TAGATGAGTTAATTCTTTGTATTTATATGGTGTGGTCACTGTCCA
1 TAGATGAGTTAATTCTTTGTATTTATATAATATGGTCACTGTCCA
26700 TAGATG
1 TAGATG
26706 TGATATGTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (45 bp):
TAGATGAGTTAATTCTTTGTATTTATATAATATGGTCACTGTCCA
Found at i:33122 original size:8 final size:8
Alignment explanation
Indices: 33109--33178 Score: 56
Period size: 8 Copynumber: 8.5 Consensus size: 8
33099 GTTTATTTAA
33109 AAAATTAT
1 AAAATTAT
33117 AAAATTAT
1 AAAATTAT
*
33125 AAAAATAT
1 AAAATTAT
33133 AAAA-TAT
1 AAAATTAT
33140 ATAAA-TAT
1 A-AAATTAT
*
33148 -AAATTTT
1 AAAATTAT
33155 AAATATTCAT
1 AAA-ATT-AT
33165 AATAATATAT
1 AA-AAT-TAT
33175 AAAA
1 AAAA
33179 ATGAAAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
6 3 0.06
7 6 0.12
8 27 0.52
9 5 0.10
10 9 0.17
11 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATTAT
Found at i:33130 original size:17 final size:17
Alignment explanation
Indices: 33108--33194 Score: 67
Period size: 17 Copynumber: 5.2 Consensus size: 17
33098 AGTTTATTTA
33108 AAAAATTATAAAATTAT
1 AAAAATTATAAAATTAT
33125 AAAAA-TATAAAA-TAT
1 AAAAATTATAAAATTAT
* *
33140 ATAAA-TAT-AAATTTT
1 AAAAATTATAAAATTAT
*
33155 AAATATTCATAATAATATAT
1 AAAAATT-ATAA-AAT-TAT
*
33175 AAAAATGA-AAAATATAT
1 AAAAATTATAAAAT-TAT
33192 AAA
1 AAA
33195 TTTTAGAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 3 0.05
15 15 0.26
16 8 0.14
17 17 0.30
18 3 0.05
19 4 0.07
20 7 0.12
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (17 bp):
AAAAATTATAAAATTAT
Found at i:33916 original size:12 final size:12
Alignment explanation
Indices: 33899--33977 Score: 67
Period size: 11 Copynumber: 6.9 Consensus size: 12
33889 TTTTTTATTA
*
33899 TTTTGGTTGGTG
1 TTTTGGTTGTTG
*
33911 TTTTGG-TGCTG
1 TTTTGGTTGTTG
* *
33922 TTTT-TTTATTG
1 TTTTGGTTGTTG
33933 TTTTGG-TGTTG
1 TTTTGGTTGTTG
*
33944 TTTTTGTTGTTG
1 TTTTGGTTGTTG
**
33956 TTTT-GTTGCAG
1 TTTTGGTTGTTG
33967 TTTTGGTTGTT
1 TTTTGGTTGTT
33978 TGGATGTTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
11 33 0.63
12 19 0.37
ACGTcount: A:0.03, C:0.03, G:0.29, T:0.66
Consensus pattern (12 bp):
TTTTGGTTGTTG
Found at i:33934 original size:22 final size:23
Alignment explanation
Indices: 33909--33970 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
33899 TTTTGGTTGG
33909 TGTTTTGGTGCTGTTTTT-TTAT
1 TGTTTTGGTGCTGTTTTTGTTAT
* *
33931 TGTTTTGGTGTTGTTTTTGTTGT
1 TGTTTTGGTGCTGTTTTTGTTAT
* *
33954 TGTTTTGTTGCAGTTTT
1 TGTTTTGGTGCTGTTTT
33971 GGTTGTTTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.03, C:0.03, G:0.26, T:0.68
Consensus pattern (23 bp):
TGTTTTGGTGCTGTTTTTGTTAT
Found at i:33959 original size:34 final size:34
Alignment explanation
Indices: 33877--33947 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
33867 GTTTTTCTAC
33877 TGTTTTGGTGC--TTTTTTTATTATTTTGGTTGG
1 TGTTTTGGTGCTGTTTTTTTATTATTTTGGTTGG
* *
33909 TGTTTTGGTGCTGTTTTTTTATTGTTTTGG-TGT
1 TGTTTTGGTGCTGTTTTTTTATTATTTTGGTTGG
33942 TGTTTT
1 TGTTTT
33948 TGTTGTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 11 0.31
33 8 0.23
34 16 0.46
ACGTcount: A:0.04, C:0.03, G:0.25, T:0.68
Consensus pattern (34 bp):
TGTTTTGGTGCTGTTTTTTTATTATTTTGGTTGG
Found at i:33976 original size:23 final size:23
Alignment explanation
Indices: 33899--33977 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 23
33889 TTTTTTATTA
*
33899 TTTTGGTTGGTGTTTTGGTGCTG
1 TTTTGGTTGTTGTTTTGGTGCTG
* * *
33922 TTTT-TTTATTGTTTTGGTGTTG
1 TTTTGGTTGTTGTTTTGGTGCTG
* * *
33944 TTTTTGTTGTTGTTTTGTTGCAG
1 TTTTGGTTGTTGTTTTGGTGCTG
33967 TTTTGGTTGTT
1 TTTTGGTTGTT
33978 TGGATGTTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
22 18 0.40
23 27 0.60
ACGTcount: A:0.03, C:0.03, G:0.29, T:0.66
Consensus pattern (23 bp):
TTTTGGTTGTTGTTTTGGTGCTG
Found at i:34514 original size:8 final size:8
Alignment explanation
Indices: 34501--34571 Score: 51
Period size: 8 Copynumber: 8.8 Consensus size: 8
34491 GTTTATTTAA
34501 AAAATTAT
1 AAAATTAT
34509 AAAATTAT
1 AAAATTAT
34517 AAAA-TAT
1 AAAATTAT
34524 ATAAA-TAT
1 A-AAATTAT
*
34532 -AAATTTT
1 AAAATTAT
34539 AAAAATTCAT
1 -AAAATT-AT
34549 AATAATATAT
1 AA-AAT-TAT
*
34559 AAAAAT-T
1 AAAATTAT
34566 AAAATT
1 AAAATT
34572 TTATAAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
6 3 0.06
7 12 0.23
8 19 0.37
9 9 0.17
10 8 0.15
11 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATTAT
Found at i:34532 original size:15 final size:16
Alignment explanation
Indices: 34501--34571 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 16
34491 GTTTATTTAA
34501 AAAATTATAAAATTAT
1 AAAATTATAAAATTAT
34517 AAAA-TATATAAA-TAT
1 AAAATTATA-AAATTAT
*
34532 -AAATTTTAAAAATTCAT
1 AAAATTAT-AAAATT-AT
*
34549 AATAATATATAAAAAT-T
1 AA-AAT-TATAAAATTAT
34566 AAAATT
1 AAAATT
34572 TTATAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 17
0.69 0.05 0.27
Matches are distributed among these distances:
14 3 0.07
15 13 0.30
16 12 0.27
17 5 0.11
18 1 0.02
19 8 0.18
20 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATTATAAAATTAT
Found at i:34571 original size:35 final size:32
Alignment explanation
Indices: 34501--34579 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
34491 GTTTATTTAA
* *
34501 AAAATTAT-AAAATTATAAAATATATAAATAT
1 AAAATTTTAAAAATTATAAAATATATAAAAAT
34532 -AAATTTTAAAAATTCATAATAATATATAAAAATT
1 AAAATTTTAAAAATT-ATAA-AATATATAAAAA-T
34566 AAAATTTTATAAAA
1 AAAATTTTA-AAAA
34580 ATGAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 6 0.15
31 6 0.15
32 4 0.10
33 11 0.28
34 1 0.03
35 8 0.20
36 4 0.10
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (32 bp):
AAAATTTTAAAAATTATAAAATATATAAAAAT
Found at i:34577 original size:27 final size:26
Alignment explanation
Indices: 34509--34569 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
34499 AAAAAATTAT
34509 AAAATTATAAAA-T-AT-ATAAATATA
1 AAAATTA-AAAATTCATAATAAATATA
**
34533 AATTTTAAAAATTCATAATAATATATA
1 AAAATTAAAAATTCATAATAA-ATATA
34560 AAAATTAAAA
1 AAAATTAAAA
34570 TTTTATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 4 0.14
24 6 0.21
25 2 0.07
26 4 0.14
27 13 0.45
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAATTAAAAATTCATAATAAATATA
Found at i:34992 original size:13 final size:13
Alignment explanation
Indices: 34974--35038 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
34964 GTCAAAGGTA
34974 TTTTTTAAATATT
1 TTTTTTAAATATT
*
34987 TTTTTTTAATATT
1 TTTTTTAAATATT
* * * * *
35000 CTTGTCAAATGTA
1 TTTTTTAAATATT
*
35013 TTTTTAAAATATT
1 TTTTTTAAATATT
35026 TATTTTT-AATATT
1 T-TTTTTAAATATT
35039 CTTGAATTTA
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
13 34 0.89
14 4 0.11
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (13 bp):
TTTTTTAAATATT
Found at i:35023 original size:39 final size:39
Alignment explanation
Indices: 34964--35042 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
34954 GACTTGCAAA
* *
34964 GTCAAAGGTATTTTTTAAATATTTTTTTTTAATATTCTT
1 GTCAAAGGTATTTTTAAAATATTTATTTTTAATATTCTT
*
35003 GTCAAATGTATTTTTAAAATATTTATTTTTAATATTCTT
1 GTCAAAGGTATTTTTAAAATATTTATTTTTAATATTCTT
35042 G
1 G
35043 AATTTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (39 bp):
GTCAAAGGTATTTTTAAAATATTTATTTTTAATATTCTT
Found at i:35309 original size:22 final size:22
Alignment explanation
Indices: 35283--35356 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
35273 TTTATTGTTG
*
35283 TTTTGGTGTTTTTTTTTTACTG
1 TTTTGGTGTTTTTTTTTTACTA
*
35305 TTTTGGT-TGTTTTTTTTTGCTA
1 TTTTGGTGT-TTTTTTTTTACTA
* * *
35327 TTTTGATATTGTTTTTTTACTA
1 TTTTGGTGTTTTTTTTTTACTA
35349 TTTTGGTG
1 TTTTGGTG
35357 CTTTATTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.02
22 41 0.95
23 1 0.02
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (22 bp):
TTTTGGTGTTTTTTTTTTACTA
Found at i:35403 original size:21 final size:20
Alignment explanation
Indices: 35378--35423 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
35368 ATTTTGGTTG
35378 CTGTTTTGGTGCTGATTTTTA
1 CTGTTTTGGTGCTG-TTTTTA
* * *
35399 CTGTTTTTGTGTTGTTTTTG
1 CTGTTTTGGTGCTGTTTTTA
35419 CTGTT
1 CTGTT
35424 ATTTTTGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.04, C:0.09, G:0.24, T:0.63
Consensus pattern (20 bp):
CTGTTTTGGTGCTGTTTTTA
Found at i:35423 original size:12 final size:12
Alignment explanation
Indices: 35400--35451 Score: 63
Period size: 11 Copynumber: 4.5 Consensus size: 12
35390 TGATTTTTAC
35400 TGTTTTTG-TGT
1 TGTTTTTGCTGT
35411 TGTTTTTGCTGT
1 TGTTTTTGCTGT
* *
35423 TATTTTTGTTGT
1 TGTTTTTGCTGT
*
35435 TG-TTTTGCTGC
1 TGTTTTTGCTGT
35446 TGTTTT
1 TGTTTT
35452 CGTTGTTTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 17 0.50
12 17 0.50
ACGTcount: A:0.02, C:0.06, G:0.23, T:0.69
Consensus pattern (12 bp):
TGTTTTTGCTGT
Found at i:35440 original size:23 final size:24
Alignment explanation
Indices: 35402--35458 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
35392 ATTTTTACTG
*
35402 TTTTTG-TGTTGTTTTTGCTGTTA
1 TTTTTGTTGTTGTTTTTGCTGCTA
*
35425 TTTTTGTTGTTG-TTTTGCTGCTG
1 TTTTTGTTGTTGTTTTTGCTGCTA
*
35448 TTTTCGTTGTT
1 TTTTTGTTGTT
35459 TGGATGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.02, C:0.07, G:0.23, T:0.68
Consensus pattern (24 bp):
TTTTTGTTGTTGTTTTTGCTGCTA
Found at i:36025 original size:15 final size:15
Alignment explanation
Indices: 35983--36025 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
35973 TTTATTTAAA
*
35983 AAATTATAAAATTAT
1 AAATTATAAAAATAT
* *
35998 AAAATATATAAATAT
1 AAATTATAAAAATAT
*
36013 AAATTTTAAAAAT
1 AAATTATAAAAAT
36026 TCTTAATAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTATAAAAATAT
Found at i:44485 original size:17 final size:17
Alignment explanation
Indices: 44465--44523 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
44455 TCAACATGAT
44465 TAAATAATTCAATAATA
1 TAAATAATTCAATAATA
* * *
44482 TAAAAAATACAA-AATG
1 TAAATAATTCAATAATA
44498 TGAAATTTAATTCAATAATA
1 T-AAA--TAATTCAATAATA
44518 TAAATA
1 TAAATA
44524 GTAAACATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 4 0.12
17 15 0.47
19 9 0.28
20 4 0.12
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:44723 original size:54 final size:51
Alignment explanation
Indices: 44568--44756 Score: 154
Period size: 54 Copynumber: 3.6 Consensus size: 51
44558 TGGGGGGGGT
* * *
44568 GGTTGGGAGGAAGTAAAAATTTTGGGGAAAGCAAAAAGAAAAAAAGTTTTTGG
1 GGTT-GGAGGAAGTAAAAATTTTGGGGGAAGAAAAAAGGAAAAAAG-TTTTGG
* * *
44621 GGTTTGAAGGAAGT--AAGTTTCGGGGGAA-AACAAAAGGAAGAAAA-TTTTGAG
1 GG-TTGGAGGAAGTAAAAATTTTGGGGGAAGAA-AAAAGGAA-AAAAGTTTTG-G
**
44672 GGTTGGAGGAAGTAAAAATTTTGAGGGGCAAGTTAAAAGGAAAAAAGTTTTGGGG
1 GGTTGGAGGAAGTAAAAATTTTG-GGGG-AAGAAAAAAGGAAAAAAGTTTT--GG
*
44727 GGTT-TAGGAAGTAAAAATTTTTGGGCGGAA
1 GGTTGGAGGAAGTAAAAA-TTTTGGG-GGAA
44757 AGTAAATGTT
Statistics
Matches: 110, Mismatches: 12, Indels: 27
0.74 0.08 0.18
Matches are distributed among these distances:
50 16 0.15
51 21 0.19
52 10 0.09
53 18 0.16
54 32 0.29
55 12 0.11
56 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.34, T:0.24
Consensus pattern (51 bp):
GGTTGGAGGAAGTAAAAATTTTGGGGGAAGAAAAAAGGAAAAAAGTTTTGG
Found at i:46107 original size:27 final size:27
Alignment explanation
Indices: 46076--46161 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
46066 CAAACCAACG
*
46076 ATAACTATAATTATTAAATAAAATATA
1 ATAACTATAATAATTAAATAAAATATA
* *
46103 ATAACTATTATAATGAAATAAAATATA
1 ATAACTATAATAATTAAATAAAATATA
* * * * *
46130 TTAATTACAATAATTATAATGAAATAAA
1 ATAACTATAATAATTA-AATAAAATATA
46158 ATAA
1 ATAA
46162 AATAATTGTA
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
27 35 0.74
28 12 0.26
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (27 bp):
ATAACTATAATAATTAAATAAAATATA
Found at i:46127 original size:22 final size:21
Alignment explanation
Indices: 46082--46127 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
46072 AACGATAACT
* *
46082 ATAATTATTAAATAAAATATA
1 ATAACTATTAAATAAAATAAA
*
46103 ATAACTATTATAATGAAATAAA
1 ATAACTATTA-AATAAAATAAA
46125 ATA
1 ATA
46128 TATTAATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAACTATTAAATAAAATAAA
Found at i:46257 original size:153 final size:153
Alignment explanation
Indices: 46067--46370 Score: 536
Period size: 153 Copynumber: 2.0 Consensus size: 153
46057 ACATGATTGC
46067 AAACCAACGATAACTATAATTATTAAATAAAATATAATAACTATTATAATGAAATAAAATATATT
1 AAACCAACGATAACTATAATTATTAAATAAAATATAATAACTATTATAATGAAATAAAATATATT
* *
46132 AATTACAATAATTATAATGAAATAAAATAAAATAATTGTAATGTATGGTAGATTCATTATTAAGA
66 AATTACAATAATTATAATGAAATAAAATAAAATAATTGTAATGTATGGAAGATTCATTAGTAAGA
*
46197 CTATTTTAATTAATTTTAAATAA
131 CTATTTTAATTAATATTAAATAA
*
46220 AAACCAACGATATCTATAATTATTAAATAAAATATAATAACTATTATAATGAAATAAAATATATT
1 AAACCAACGATAACTATAATTATTAAATAAAATATAATAACTATTATAATGAAATAAAATATATT
* * *
46285 AATTATAATAATTATAATGAAATGAAATAAAATAATTGTAATTTATGGAAGATTCATTAGTAAGA
66 AATTACAATAATTATAATGAAATAAAATAAAATAATTGTAATGTATGGAAGATTCATTAGTAAGA
*
46350 TTATTTTAATTAATATTAAAT
131 CTATTTTAATTAATATTAAAT
46371 TTTATTTAAA
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
153 143 1.00
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (153 bp):
AAACCAACGATAACTATAATTATTAAATAAAATATAATAACTATTATAATGAAATAAAATATATT
AATTACAATAATTATAATGAAATAAAATAAAATAATTGTAATGTATGGAAGATTCATTAGTAAGA
CTATTTTAATTAATATTAAATAA
Found at i:46274 original size:27 final size:27
Alignment explanation
Indices: 46233--46296 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
46223 CCAACGATAT
* *
46233 CTATAATTATTAAATAAAATATAATAA
1 CTATAATAATGAAATAAAATATAATAA
* *
46260 CTATTATAATGAAATAAAATATATTAA
1 CTATAATAATGAAATAAAATATAATAA
*
46287 TTATAATAAT
1 CTATAATAAT
46297 TATAATGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (27 bp):
CTATAATAATGAAATAAAATATAATAA
Found at i:46321 original size:33 final size:32
Alignment explanation
Indices: 46244--46330 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
46234 TATAATTATT
*
46244 AAATAAAAT-ATAATAACTATTATAATGAAATA
1 AAATAAAATAATTATAA-TATTATAATGAAATA
* * *
46276 AAATATATTAATTATAATAATTATAATGAAATG
1 AAATAAAATAATTATAAT-ATTATAATGAAATA
*
46309 AAATAAAATAATTGTAAT-TTAT
1 AAATAAAATAATTATAATATTAT
46331 GGAAGATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 4 0.09
32 8 0.17
33 34 0.74
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (32 bp):
AAATAAAATAATTATAATATTATAATGAAATA
Found at i:62502 original size:27 final size:27
Alignment explanation
Indices: 62462--62585 Score: 140
Period size: 27 Copynumber: 4.6 Consensus size: 27
62452 AAGTTTGAGC
*
62462 AATGAGCGAATATTCTGTATATGGCTCG
1 AATGAGCG-ATATTCTGTATCTGGCTCG
* * **
62490 AATGAACGATATTTTGTATCTGGCTTT
1 AATGAGCGATATTCTGTATCTGGCTCG
* * *
62517 AATTAGCGATATTCTTTATCTGGCTTG
1 AATGAGCGATATTCTGTATCTGGCTCG
*
62544 AATGAGCGATATTCTGTATGTGGCTCG
1 AATGAGCGATATTCTGTATCTGGCTCG
* *
62571 AATAAGCGGTATTCT
1 AATGAGCGATATTCT
62586 ATTACTGCTG
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
27 73 0.91
28 7 0.09
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (27 bp):
AATGAGCGATATTCTGTATCTGGCTCG
Found at i:62584 original size:54 final size:54
Alignment explanation
Indices: 62466--62601 Score: 143
Period size: 54 Copynumber: 2.5 Consensus size: 54
62456 TTGAGCAATG
* * * * * ** *
62466 AGCGAATATTCTGTATATGGCTCGAATGAACGATATTTTGTATCTGGCTTTAATT
1 AGCG-ATATTCTTTATCTGGCTTGAATGAGCGATATTCTGTATCTGGCTCGAATA
*
62521 AGCGATATTCTTTATCTGGCTTGAATGAGCGATATTCTGTATGTGGCTCGAATA
1 AGCGATATTCTTTATCTGGCTTGAATGAGCGATATTCTGTATCTGGCTCGAATA
*
62575 AGCGGTATTCTATTA-CT-GC-TGAATGAG
1 AGCGATATTCT-TTATCTGGCTTGAATGAG
62602 ATCATGCATA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
52 8 0.11
53 2 0.03
54 53 0.76
55 7 0.10
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (54 bp):
AGCGATATTCTTTATCTGGCTTGAATGAGCGATATTCTGTATCTGGCTCGAATA
Found at i:68484 original size:26 final size:25
Alignment explanation
Indices: 68449--68500 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
68439 TTTCATTTTA
68449 ATTCAATTCATTT-TTTTTCTTTCAAT
1 ATTCAATTCATTTATTTTT-TTT-AAT
*
68475 ATTCGATTCATTTATTTTTTTTAAT
1 ATTCAATTCATTTATTTTTTTTAAT
68500 A
1 A
68501 AGGAAAGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 15 0.62
27 5 0.21
ACGTcount: A:0.25, C:0.12, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTCAATTCATTTATTTTTTTTAAT
Found at i:72761 original size:15 final size:15
Alignment explanation
Indices: 72743--72776 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
72733 AATGTAAATT
*
72743 AAATAAAAAATAATA
1 AAATAAAAAACAATA
*
72758 AAATAAATAACAATA
1 AAATAAAAAACAATA
72773 AAAT
1 AAAT
72777 GACATGAAAA
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:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAAAAAACAATA
Found at i:72823 original size:17 final size:16
Alignment explanation
Indices: 72801--72838 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
72791 TAACAACTAG
72801 ATAAATAAACAA-AGAAA
1 ATAAATAAA-AATA-AAA
72818 ATAAATAAAAATAAAA
1 ATAAATAAAAATAAAA
72834 ATAAA
1 ATAAA
72839 ATGCTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (16 bp):
ATAAATAAAAATAAAA
Found at i:72877 original size:13 final size:14
Alignment explanation
Indices: 72844--72877 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
72834 ATAAAATGCT
72844 AAAATAAACAAATA
1 AAAATAAACAAATA
*
72858 AATATAAAC-AATA
1 AAAATAAACAAATA
72871 AAAATAA
1 AAAATAA
72878 TTAGGATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATAAACAAATA
Found at i:72927 original size:15 final size:15
Alignment explanation
Indices: 72893--72934 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
72883 ATTAGGCATG
*
72893 AAAATAAAT-GACAA
1 AAAATAAATAAACAA
72907 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
*
72923 AAAATTAATAAA
1 AAAATAAATAAA
72935 TTAAAGGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:73187 original size:22 final size:23
Alignment explanation
Indices: 73150--73206 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
73140 TGTATGCCTC
* * *
73150 AAAAAAATTCTCTGAATGTT-GT
1 AAAAAAAATCTTTGAATCTTAGT
* *
73172 ATAAAAAATCTTTGAATCTTATT
1 AAAAAAAATCTTTGAATCTTAGT
73195 AAAAAAAATCTT
1 AAAAAAAATCTT
73207 CCTTCTCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (23 bp):
AAAAAAAATCTTTGAATCTTAGT
Found at i:73870 original size:50 final size:51
Alignment explanation
Indices: 73816--73929 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 51
73806 CCTCTACAGC
* * * * * *
73816 TTTAGGGGTATAAGAATT-GTCATTACAGTTTTAATTTGTCCCTCTTTGGT
1 TTTAGAGGTATAAGAATTCGCCATTACAGCTTCAATCTATCCCTCTTTGGT
* * *
73866 TTTAGAGGTGTAAG-ATTCGCCTTTGCAGCTTCAATCTATCCCTCTTTGGT
1 TTTAGAGGTATAAGAATTCGCCATTACAGCTTCAATCTATCCCTCTTTGGT
73916 TTTA-AGGTATAAGA
1 TTTAGAGGTATAAGA
73930 TTTACCGTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
49 11 0.21
50 41 0.79
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (51 bp):
TTTAGAGGTATAAGAATTCGCCATTACAGCTTCAATCTATCCCTCTTTGGT
Found at i:74474 original size:50 final size:50
Alignment explanation
Indices: 73904--74598 Score: 497
Period size: 49 Copynumber: 14.2 Consensus size: 50
73894 CTTCAATCTA
* * * * ** *
73904 TCCCTCTTTGGTTTTAAGGTATAAGATTTACCGTTACGACTTTAAT-TTG
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
* * * *
73953 TCTCTCTTCAATTTAAAGGGTGTAAGATTTGTCG-T--GACTTTAATC-TA
1 TCCCTCTTCGATTT-TAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
* * * ** * * * * *
74000 TCCCT-TTATGATTTTAAGGTGTAAAATTCATCTTTGC-AGTTTTGA-CCTT
1 TCCCTCTT-CGATTTTAGGGTGTAAGATTTGTCGTTACGA-CTTTAATCTTT
* *
74049 TCCCTCTTC-AGTTTTAGGGTGTAAGATTTG-CCTTACGGCTTTAATC-TT
1 TCCCTCTTCGA-TTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
* ** * * * *
74097 TCCCTCTTCGATTTTAGTGTGTAAGATCCGACATTGCAACTTTAATC-TT
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
* * * * * *
74146 TCCCTCTTCGATTTTAAGGTGTTAGATTCGCCATTATGACTTTAATC-TT
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
* * * *
74195 TCCCTCTTCGATTTTAGGGTGTAAGATTTG-CTGCTATGGCTTTAATC-TA
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTC-GTTACGACTTTAATCTTT
** **
74244 TCCCT-TTTTAGTTTTAGGGTGTAAGATTTACCGTTACGACTTTAATCTTT
1 TCCCTCTTCGA-TTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
* * ** **
74294 T-CCTCTTTGGTTTTAGGGTGTAAGATTCATAATTACGACTTTAATC-TT
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
* *
74342 T-CC-C-TC-ATTTTAGGTTATAAGATTTGTCGTT--GTAGCTTTAATCTTT
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTCGTTACG-A-CTTTAATCTTT
* * ** *
74388 T-CCTTTTCGATTTTAAGGTGTAAGATTCATCGTTGCGACTTTAATCTTT
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
* * * * * * *
74437 TCCCTTTTTGATTTTAGGGTGTAAAATTTGTCATTGCGACTTTGATTTTT
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
* *
74487 TCCCTCTTCGATTTTAAGGTGTAAGATTTG-CTGTTACAACTTTAATCTTT
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTC-GTTACGACTTTAATCTTT
* ** *
74537 TCCCTCTTCGATTTTAGGGTGTAAAATTCATCGTTACGGCTTTAATCTTT
1 TCCCTCTTCGATTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
74587 TCCCTCTTCGAT
1 TCCCTCTTCGAT
74599 CCTTACAACT
Statistics
Matches: 512, Mismatches: 104, Indels: 59
0.76 0.15 0.09
Matches are distributed among these distances:
43 1 0.00
44 1 0.00
45 26 0.05
46 21 0.04
47 20 0.04
48 49 0.10
49 236 0.46
50 156 0.30
51 2 0.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.46
Consensus pattern (50 bp):
TCCCTCTTCGATTTTAGGGTGTAAGATTTGTCGTTACGACTTTAATCTTT
Found at i:83008 original size:21 final size:21
Alignment explanation
Indices: 82984--83027 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
82974 ACATATATAA
82984 AACAAAAATAAAATACAAA-GC
1 AACAAAAATAAAATA-AAATGC
* *
83005 AACATATATAAAATAAAATGC
1 AACAAAAATAAAATAAAATGC
83026 AA
1 AA
83028 AGAATCACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.68, C:0.11, G:0.05, T:0.16
Consensus pattern (21 bp):
AACAAAAATAAAATAAAATGC
Found at i:83044 original size:26 final size:26
Alignment explanation
Indices: 82988--83049 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
82978 ATATAAAACA
* *
82988 AAAATAAAATACAAAGCAACATATAT
1 AAAATAAAATACAAAGCAACACAAAT
*
83014 AAAATAAAATGCAAAG-AATCACAAAT
1 AAAATAAAATACAAAGCAA-CACAAAT
* *
83040 TAAATTAAAT
1 AAAATAAAAT
83050 CGAATTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 2 0.07
26 28 0.93
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.21
Consensus pattern (26 bp):
AAAATAAAATACAAAGCAACACAAAT
Found at i:84046 original size:16 final size:16
Alignment explanation
Indices: 84025--84065 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
84015 AAAATATGAC
84025 ATATAAATAAATAAAA
1 ATATAAATAAATAAAA
* *
84041 ATATAAATGAATAAAT
1 ATATAAATAAATAAAA
84057 ATATGAAAT
1 ATAT-AAAT
84066 GCAATCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (16 bp):
ATATAAATAAATAAAA
Found at i:84942 original size:27 final size:27
Alignment explanation
Indices: 84904--84964 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
84894 AGGCTGTAAC
*
84904 ATTCTGTATCTGGCTCGAATGAGCGAT
1 ATTCTGTATCTGGCTCGAACGAGCGAT
*
84931 ATTCTGTATCTGGCTCGAACGAGCGGT
1 ATTCTGTATCTGGCTCGAACGAGCGAT
84958 ATTCTGT
1 ATTCTGT
84965 TATTGCTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (27 bp):
ATTCTGTATCTGGCTCGAACGAGCGAT
Found at i:86758 original size:2 final size:2
Alignment explanation
Indices: 86751--86783 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
86741 TTGTTTCATT
*
86751 TA TA TA TA TT 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 TA T
86784 GTATTTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:87903 original size:30 final size:30
Alignment explanation
Indices: 87846--87904 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
87836 TAAAAAAATC
* *
87846 AGTTAAAAAATTTAATTGATGTAATTTTAA
1 AGTTAAAAAATTCAATTGATATAATTTTAA
*
87876 AGTTTAAAAATTCAATTGA-ATATATTTTA
1 AGTTAAAAAATTCAATTGATATA-ATTTTA
87905 TATAGAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (30 bp):
AGTTAAAAAATTCAATTGATATAATTTTAA
Found at i:89801 original size:18 final size:17
Alignment explanation
Indices: 89759--89801 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
89749 CTTCAGAGTA
89759 TTATTTAA-TGTTTTTT
1 TTATTTAATTGTTTTTT
*
89775 TT-TTAAATTAGTTTTTT
1 TTATTTAATT-GTTTTTT
89792 TTATTTAATT
1 TTATTTAATT
89802 TGATATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 4 0.18
16 3 0.14
17 9 0.41
18 6 0.27
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
TTATTTAATTGTTTTTT
Found at i:89814 original size:27 final size:27
Alignment explanation
Indices: 89784--89862 Score: 68
Period size: 33 Copynumber: 2.7 Consensus size: 27
89774 TTTTTAAATT
*
89784 AGTTTTTTTTATTTAATTTGATATTTG
1 AGTTTTTTTTATTTAATTTGATATTTA
89811 AGTTTGATATTTTTATTTTTAATTTGATATTTA
1 AG-TT--T-TTTTTA--TTTAATTTGATATTTA
** *
89844 AAATTTTTTTATCTAATTT
1 AGTTTTTTTTATTTAATTT
89863 TATACTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
27 9 0.21
28 2 0.05
29 6 0.14
30 2 0.05
31 6 0.14
32 1 0.02
33 16 0.38
ACGTcount: A:0.27, C:0.01, G:0.08, T:0.65
Consensus pattern (27 bp):
AGTTTTTTTTATTTAATTTGATATTTA
Found at i:91827 original size:18 final size:18
Alignment explanation
Indices: 91804--91839 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
91794 TCCCAAAGTA
91804 AGCATGTGTATCTATATG
1 AGCATGTGTATCTATATG
91822 AGCATGTGTATCTATATG
1 AGCATGTGTATCTATATG
91840 CACATCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (18 bp):
AGCATGTGTATCTATATG
Found at i:93452 original size:20 final size:20
Alignment explanation
Indices: 93429--93468 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
93419 TTAATTAACA
*
93429 TAATTAACCTTACTTTAATT
1 TAATAAACCTTACTTTAATT
* *
93449 TAATAAACTTTATTTTAATT
1 TAATAAACCTTACTTTAATT
93469 AAGTTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATAAACCTTACTTTAATT
Found at i:97533 original size:59 final size:59
Alignment explanation
Indices: 97461--97580 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
97451 GAAAGCATAC
97461 ATTTGAGTTTATCTTAGATTAAACACTTTTACAATAGTAATATTAATTAATTATTAATA
1 ATTTGAGTTTATCTTAGATTAAACACTTTTACAATAGTAATATTAATTAATTATTAATA
*
97520 ATTTGAGTTTATCTTAGATTAAACATTTTTACAATAGTAATATTAATTAATTATTAATA
1 ATTTGAGTTTATCTTAGATTAAACACTTTTACAATAGTAATATTAATTAATTATTAATA
97579 AT
1 AT
97581 AGATAAGATA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.47
Consensus pattern (59 bp):
ATTTGAGTTTATCTTAGATTAAACACTTTTACAATAGTAATATTAATTAATTATTAATA
Found at i:98306 original size:16 final size:17
Alignment explanation
Indices: 98285--98316 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
98275 AAATATAAAA
98285 TAATAAATAT-TTATAT
1 TAATAAATATATTATAT
98301 TAATAAATATATTATA
1 TAATAAATATATTATA
98317 CATATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATAAATATATTATAT
Found at i:98324 original size:20 final size:17
Alignment explanation
Indices: 98284--98327 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
98274 TAAATATAAA
98284 ATAATAAATATTTATAT
1 ATAATAAATATTTATAT
98301 -TAATAAATATATTATACAT
1 ATAATAAATAT-TTAT--AT
98320 ATAATAAA
1 ATAATAAA
98328 CACACAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 10 0.43
17 4 0.17
19 2 0.09
20 7 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATAAATATTTATAT
Found at i:99043 original size:24 final size:23
Alignment explanation
Indices: 99005--99054 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
98995 TTAATATATG
* *
99005 AAATATTAATTTTAAATATTTTT
1 AAATATTAATATTAAATATTTAT
*
99028 AAATAATTAATATTAATTATTTAT
1 AAAT-ATTAATATTAAATATTTAT
99052 AAA
1 AAA
99055 ATCTAATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTAT
Done.