Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014292.1 Corchorus olitorius cultivar O-4 contig14325, 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: 64280
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1098 original size:204 final size:205
Alignment explanation
Indices: 746--1159 Score: 796
Period size: 204 Copynumber: 2.0 Consensus size: 205
736 GCTTAATAAC
746 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACTAAAGTTGTAGTAGAAT
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACTAAAGTTGTAGTAGAAT
811 AAGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTG
66 AAGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTG
*
876 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATATAAGATATTAAA
131 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AA
941 GATCCGATTTA
195 GATCCGATTTA
952 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAAC-AAAGTTGTAGT-GAAT
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACTAAAGTTGTAGTAGAAT
1015 AAGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTG
66 AAGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTG
1080 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
131 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
1145 ATCCGATTTA
196 ATCCGATTTA
1155 TTTAT
1 TTTAT
1160 TATTAAGGAA
Statistics
Matches: 207, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
203 18 0.09
204 130 0.63
205 11 0.05
206 48 0.23
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (205 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACTAAAGTTGTAGTAGAAT
AAGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTG
GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
ATCCGATTTA
Found at i:1323 original size:39 final size:40
Alignment explanation
Indices: 1269--1349 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
1259 ATACCTAAGA
*
1269 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
1308 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
1348 AT
1 AT
1350 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:2623 original size:20 final size:20
Alignment explanation
Indices: 2586--2624 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2576 TGCTATTATT
2586 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
2606 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
2625 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:2893 original size:66 final size:66
Alignment explanation
Indices: 2787--2971 Score: 196
Period size: 66 Copynumber: 2.8 Consensus size: 66
2777 TCTTGTCTCT
* * * * * * *
2787 GTGTGGTTATCAAAATTTCGTACGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAA-TTCT
1 GTGTGGTTACCAAAATTTCATACGATAGTTATCAAAATTTCATG-GGAAGGTCACCAAAATTTC-
2850 ATA
64 ATA
*
2853 GTGTGGTTACCAAAATTTCATATG-TAAGTTATCAAAATTTCATGGGAAGGTCACCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATACGAT-AGTTATCAAAATTTCATGGGAAGGTCACCAAAATTTCA
2917 TA
65 TA
* * * *
2919 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAAGGT
1 GTGTGGTTACCAAAATTTCATACGAT-A-GTTATCAAAATTTCATGGGAAGGT
2972 TATTGGAATT
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
65 3 0.03
66 72 0.71
67 5 0.05
68 21 0.21
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATACGATAGTTATCAAAATTTCATGGGAAGGTCACCAAAATTTCAT
A
Found at i:2974 original size:22 final size:22
Alignment explanation
Indices: 2791--3023 Score: 143
Period size: 22 Copynumber: 10.5 Consensus size: 22
2781 GTCTCTGTGT
* * *
2791 GGTTATCAAAATTTCGTACGAT
1 GGTTATCAAAATTTCATAGGAA
* *
2813 GGTTATTATAATTTCATGAGG-A
1 GGTTATCAAAATTTCAT-AGGAA
*
2835 GGTTATCAAAA-TTCTATAGTG-T
1 GGTTATCAAAATTTC-ATAG-GAA
* *
2857 GGTTACCAAAATTTCATATGTAA
1 GGTTATCAAAATTTCATA-GGAA
*
2880 -GTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGGAA
* * *
2901 GGTCACCAAAATTTCATAGTG-T
1 GGTTATCAAAATTTCATAG-GAA
*
2923 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGGA--A
* *
2947 GGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGGAA
*** ** *
2969 GGTTATTGGAATTTCATAATAT
1 GGTTATCAAAATTTCATAGGAA
* * *
2991 GGTTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAGGAA
*
3013 AGTTATCAAAA
1 GGTTATCAAAA
3024 AGTGATTATC
Statistics
Matches: 162, Mismatches: 38, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
21 9 0.06
22 128 0.79
23 7 0.04
24 18 0.11
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGGAA
Found at i:3151 original size:44 final size:43
Alignment explanation
Indices: 3029--3814 Score: 265
Period size: 44 Copynumber: 18.3 Consensus size: 43
3019 CAAAAAGTGA
* * * *
3029 TTATCAAAATGTCATAGCGAGATTAT-AAGAATTTCATAGTGCGG
1 TTATCAAAATTTCATAG-GAGGTTATCAA-AATTTCATAGGGAGG
* * *
3073 TTAACAAAATTTCATAAGGAGGTTA-CTAATATTTCATGGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTATC-AAAATTTCATAGGGAGG
* * *
3117 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGGGAGG
* ** * * *
3161 TTATAAAAGTCTCAATTTCATAAAAAG-TATCAACA-TTCGATA-GAAGG
1 TTAT-CAA-----AATTTCATAGGAGGTTATCAAAATTTC-ATAGGGAGG
* * *
3208 TTATC-AAATCTCATA-GAGTGATTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGGAG-G-TTATCAAAATTTCATAGGGA--GG
* * * **
3253 ATTATCAAAATTT-ATAGGAAGATTATTAAAATTTCATAGCGTTG
1 -TTATCAAAATTTCATAGG-AGGTTATCAAAATTTCATAGGGAGG
* ** * ** * *
3297 TTATCAAAATTTCAAAACAAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTC-ATAGGAGGTTATCAAAATTTCATAGGGAGG
* * * * * *
3341 TTATCAAAATTT-TTAGAGGGGTCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGGGAGG
* * * ** * *
3384 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGGGAGG
* * * *
3428 TTACCAATATTTCATA-GTGG---T----ATTTC-TGGGGAGG
1 TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGGGAGG
* * * *
3462 TTTTCAAAATTTCATAGTATGGTTA-CCAAA--T--TAGGAAGG
1 TTATCAAAATTTCATAGGA-GGTTATCAAAATTTCATAGGGAGG
* * * *
3501 TTATTAAACTTTTATTATGGA-GTAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCA-TA-GGAGGTTATCAAAATTTCATAGGGAGG
* **
3543 TTATCAAAATTTCATAGTTTA-GTT-TCAAAATTTCATA-AAAGGG
1 TTATCAAAATTTCATAG--GAGGTTATCAAAATTTCATAGGGA-GG
* * * *
3586 TTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGGAGGT-TATCAAAATTTCATAGGGAGG
* * * *** * *
3630 TTAACAAAATTTCATAATGAGGTTATAAAAAAAACATAGGAAGA
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGGGAGG
* * * *
3674 TTATCAAAA-TT--T-GTA-GTTATCAAGATTTTATAAGGAGG
1 TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGGGAGG
* * * *
3712 -TATCAAAATTTTATAGGGAGTTTTATCAAAATTTTATAGGAAGG
1 TTATCAAAATTTCATA-GGAG-GTTATCAAAATTTCATAGGGAGG
* * * *
3756 TTTATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTGTGA
1 -TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGGGAGG
*
3801 TTATCAAGATTTCA
1 TTATCAAAATTTCA
3815 GACTGTGATT
Statistics
Matches: 538, Mismatches: 141, Indels: 126
0.67 0.18 0.16
Matches are distributed among these distances:
34 15 0.03
35 4 0.01
36 2 0.00
37 8 0.01
38 16 0.03
39 22 0.04
40 18 0.03
41 17 0.03
42 40 0.07
43 69 0.13
44 211 0.39
45 35 0.07
46 41 0.08
47 18 0.03
48 12 0.02
49 1 0.00
50 9 0.02
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGGGAGG
Found at i:3164 original size:22 final size:21
Alignment explanation
Indices: 3029--3419 Score: 154
Period size: 22 Copynumber: 17.7 Consensus size: 21
3019 CAAAAAGTGA
* * *
3029 TTATCAAAATGTCATAGCGAGA
1 TTATCAAAATTTCATAG-AAGG
**
3051 TTAT-AAGAATTTCATAGTGCGG
1 TTATCAA-AATTTCATAG-AAGG
* *
3073 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGAAGG
* * *
3095 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGAAGG
**
3117 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-AAGG
3139 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GAAGG
* * *
3161 TTATAAAAGTCTCAATTTCATAAAAAG
1 TTAT-CAA-----AATTTCATAGAAGG
*
3188 -TATCAACA-TTCGATAGAAGG
1 TTATCAAAATTTC-ATAGAAGG
*
3208 TTATC-AAATCTCATAG-AGTG
1 TTATCAAAATTTCATAGAAG-G
*
3228 ATTATCGAAATTTCATAGAGATCGG
1 -TTATCAAAATTTCATAGA-A--GG
*
3253 ATTATCAAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATA-GAAGG
* *
3275 TTATTAAAATTTCATAG-CGTTG
1 TTATCAAAATTTCATAGAAG--G
* *
3297 TTATCAAAATTTCAAAACAAGG
1 TTATCAAAATTTC-ATAGAAGG
* *
3319 TTATCAAAATTACATA-ATGTG
1 TTATCAAAATTTCATAGAAG-G
* *
3340 ATTATCAAAATTT-TTAGAGGGG
1 -TTATCAAAATTTCATAGA-AGG
* * *
3362 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
3384 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
3406 TTATCAAATTTTCA
1 TTATCAAAATTTCA
3420 AAATGTGATT
Statistics
Matches: 287, Mismatches: 48, Indels: 68
0.71 0.12 0.17
Matches are distributed among these distances:
19 5 0.02
20 17 0.06
21 42 0.15
22 173 0.60
23 11 0.04
24 6 0.02
25 17 0.06
26 4 0.01
27 3 0.01
28 9 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGAAGG
Found at i:3371 original size:87 final size:87
Alignment explanation
Indices: 3280--3439 Score: 214
Period size: 87 Copynumber: 1.8 Consensus size: 87
3270 GAAGATTATT
* ** *
3280 AAAATTTCATAGCGTTGTTATCAAAATTTCA-AAACAAGGTTATCAAAATTACATAATGTGATTA
1 AAAATTTCATAGAGAGGTTATCAAAATTTCATAAA-AAGGTTATCAAAATTACAAAATGTGATTA
*
3344 TCAAAATTTTTAGAGGGGTCAAC
65 CCAAAATTTTTAGAGGGGTCAAC
* * * *
3367 AAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTAC
1 AAAATTTCATAGAGAGGTTATCAAAATTTCATAAAAAGGTTATCAAAATTACAAAATGTGATTAC
*
3432 CAATATTT
66 CAAAATTT
3440 CATAGTGGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
87 59 0.95
88 3 0.05
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (87 bp):
AAAATTTCATAGAGAGGTTATCAAAATTTCATAAAAAGGTTATCAAAATTACAAAATGTGATTAC
CAAAATTTTTAGAGGGGTCAAC
Found at i:3594 original size:43 final size:44
Alignment explanation
Indices: 3541--3623 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 44
3531 ATTTCAGGGA
*
3541 GGTTATCAAAATTTCATAGT-T-TAGTTTCAAAATTTCATAAAAG
1 GGTTATCAAAATTTCATAGTATGTAG-ATCAAAATTTCATAAAAG
3584 GGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATA
1 GGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATA
3624 GGGAGATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
43 20 0.54
44 14 0.38
45 3 0.08
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.39
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAAAAG
Found at i:3595 original size:22 final size:22
Alignment explanation
Indices: 3541--3601 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
3531 ATTTCAGGGA
****
3541 GGTTATCAAAATTTCATAGTTT
1 GGTTATCAAAATTTCATAAAAG
*
3563 AGTT-TCAAAATTTCATAAAAG
1 GGTTATCAAAATTTCATAAAAG
3584 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
3602 GTATGTAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAAAG
Found at i:3660 original size:22 final size:22
Alignment explanation
Indices: 3539--3814 Score: 101
Period size: 22 Copynumber: 12.8 Consensus size: 22
3529 AAATTTCAGG
*
3539 GAGGTTATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATA-AT
*
3562 TA-GTT-TCAAAATTTCATAA-
1 GAGGTTATCAAAATTTCATAAT
* *
3581 AAGGGTTATCAAAATTTCATAGT
1 GA-GGTTATCAAAATTTCATAAT
* * **
3604 -ATGTAGATCAAAATTTCATAGG
1 GAGGT-TATCAAAATTTCATAAT
* *
3626 GAGATTAACAAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAAT
* *** *
3648 GAGGTTATAAAAAAAACAT-AG
1 GAGGTTATCAAAATTTCATAAT
* *
3669 GAAGATTATCAAAA-TT--T-GT
1 G-AGGTTATCAAAATTTCATAAT
* * *
3688 -A-GTTATCAAGATTTTATAAG
1 GAGGTTATCAAAATTTCATAAT
* **
3708 GAGG-TATCAAAATTTTATAGG
1 GAGGTTATCAAAATTTCATAAT
* * *
3729 GAGTTTTATCAAAATTTTAT-AG
1 GAG-GTTATCAAAATTTCATAAT
**
3751 GAAGGTTTATCAAAATTTCATAGC
1 G-AGG-TTATCAAAATTTCATAAT
* *
3775 GAGGTTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATAAT
* * *
3797 GTGATTATCAAGATTTCA
1 GAGGTTATCAAAATTTCA
3815 GACTGTGATT
Statistics
Matches: 191, Mismatches: 44, Indels: 37
0.70 0.16 0.14
Matches are distributed among these distances:
16 8 0.04
17 3 0.02
19 3 0.02
21 39 0.20
22 101 0.53
23 36 0.19
24 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAT
Found at i:3742 original size:23 final size:22
Alignment explanation
Indices: 3690--3795 Score: 106
Period size: 23 Copynumber: 4.8 Consensus size: 22
3680 AAATTTGTAG
* *
3690 TTATCAAGATTTTATAAGGAG-
1 TTATCAAAATTTTATAGGGAGT
*
3711 GTATCAAAATTTTATAGGGAGTT
1 TTATCAAAATTTTATAGGGAG-T
*
3734 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGA-GT
* * *
3757 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTTATAGGGAGT
* *
3779 TTATCACAATTTCATAG
1 TTATCAAAATTTTATAG
3796 TGTGATTATC
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.25
22 17 0.24
23 36 0.50
24 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGT
Found at i:3821 original size:22 final size:22
Alignment explanation
Indices: 3779--3834 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
3769 CATAGCGAGG
* *
3779 TTATCACAATTTCATAGTGTGA
1 TTATCACAATTTCAGACTGTGA
3801 TTATCA-AGATTTCAGACTGTGA
1 TTATCACA-ATTTCAGACTGTGA
*
3823 TTACTAACAATT
1 TTA-TCACAATT
3835 CATATGGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 21 0.75
23 5 0.18
24 1 0.04
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (22 bp):
TTATCACAATTTCAGACTGTGA
Found at i:3959 original size:22 final size:21
Alignment explanation
Indices: 3934--4005 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
3924 TGGAAAGTTA
3934 TCAAAATTTCATAGTGAGGTCT
1 TCAAAATTTCATAG-GAGGTCT
* *
3956 TCAAAATTCCTTAGAGAGGT-T
1 TCAAAATTTCATAG-GAGGTCT
* *
3977 AACAAAATTTCATAAGGAGGTCA
1 -TCAAAATTTCAT-AGGAGGTCT
4000 TCAAAA
1 TCAAAA
4006 ATAGTGTAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 1 0.03
22 36 0.92
23 2 0.05
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (21 bp):
TCAAAATTTCATAGGAGGTCT
Found at i:8369 original size:22 final size:22
Alignment explanation
Indices: 8344--8392 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
8334 TAAAAAAATT
8344 ATAGGG-AGATTAACAAAATCTC
1 ATAGGGAAGATT-ACAAAATCTC
* *
8366 ATAGGGAAGGTTACAAAATTTC
1 ATAGGGAAGATTACAAAATCTC
8388 ATAGG
1 ATAGG
8393 AAGGTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (22 bp):
ATAGGGAAGATTACAAAATCTC
Found at i:8432 original size:22 final size:22
Alignment explanation
Indices: 8357--8432 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
8347 GGGAGATTAA
*
8357 CAAAATCTCATAGGGAAGGTTA-
1 CAAAATTTCATA-GGAAGGTTAT
8379 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* **
8402 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
8424 CAAAGTTTC
1 CAAAATTTC
8433 TGTTGTGCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.13
22 25 0.54
23 15 0.33
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:10470 original size:22 final size:22
Alignment explanation
Indices: 10386--10483 Score: 90
Period size: 22 Copynumber: 4.4 Consensus size: 22
10376 AGGTATAAAC
* * * *
10386 AATTTCATATGGAATTTATCAC
1 AATTTCATAGGGTAGTTATCAA
*
10408 AATTTCATA-GGTAATTATCAA
1 AATTTCATAGGGTAGTTATCAA
** *
10429 AACTTTTCATAGCATGGTTATCAA
1 AA--TTTCATAGGGTAGTTATCAA
*
10453 AATTTAATAGGGTAGTTATCAA
1 AATTTCATAGGGTAGTTATCAA
10475 AATTTCATA
1 AATTTCATA
10484 AAAATATTCA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 11 0.18
22 33 0.54
23 7 0.11
24 10 0.16
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (22 bp):
AATTTCATAGGGTAGTTATCAA
Found at i:11400 original size:22 final size:22
Alignment explanation
Indices: 11038--11476 Score: 180
Period size: 22 Copynumber: 19.5 Consensus size: 22
11028 CAGATTATTG
* *
11038 AAATTTCATAGTGTGGCTAT-A
1 AAATTTCATAGTGAGGTTATCA
* **
11059 TAAATTTCATAATTTGGTTA-CAA
1 -AAATTTCATAGTGAGGTTATC-A
* *
11082 AAATTTCATAG-AAGGTAATCA
1 AAATTTCATAGTGAGGTTATCA
* * * *
11103 AAGTTTCATATTGTGCTTATCAA
1 AAATTTCATAGTGAGGTTATC-A
** * *
11126 AAATTTCATAGTGACATTAACG
1 AAATTTCATAGTGAGGTTATCA
* *
11148 AAA-TTCTATAGGGAAGTTATCA
1 AAATTTC-ATAGTGAGGTTATCA
* *
11170 ACATTTCATAGGGAGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* *
11192 AAATTTTATAGT-ATGGTTATCC
1 AAATTTCATAGTGA-GGTTATCA
****
11214 AAATTTCATAGTGCACCAAATCA
1 AAATTTCATAGTG-AGGTTATCA
** * * *
11237 ACCTTCCGCAATTAATGTGG-TATTCA
1 AAATT--TC-A-TAGTGAGGTTA-TCA
* * *
11263 AAATTTTATATTAAGGTTATCAAA
1 AAATTTCATAGTGAGGTTATC--A
11287 ATTAATTTCATA-TAGAGGTTATCA
1 A--AATTTCATAGT-GAGGTTATCA
* *
11311 CAATTTTATAGT-ATGGTTATCA
1 AAATTTCATAGTGA-GGTTATCA
* * * *
11333 ACATTTCATAGTGTGGTGACCA
1 AAATTTCATAGTGAGGTTATCA
*
11355 AAGTTTCATAG-GATGGTTATCA
1 AAATTTCATAGTGA-GGTTATCA
*
11377 AAATTTCATAGTGTGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* *
11399 AAGTTTCACAAG-GAGGTTATCA
1 AAATTTCA-TAGTGAGGTTATCA
* * *
11421 CAATTTCTTAGGGAGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* * *
11443 AAATAAT-ATAGCGAGATTATCA
1 AAAT-TTCATAGTGAGGTTATCA
11465 AAATTTCATAGT
1 AAATTTCATAGT
11477 AAAACTATGT
Statistics
Matches: 304, Mismatches: 83, Indels: 60
0.68 0.19 0.13
Matches are distributed among these distances:
21 23 0.08
22 213 0.70
23 34 0.11
24 4 0.01
25 3 0.01
26 23 0.08
27 4 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
AAATTTCATAGTGAGGTTATCA
Found at i:11749 original size:22 final size:22
Alignment explanation
Indices: 11724--11778 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
11714 CGAAGTTAAT
* *
11724 TTATCATAATTTTATAGAGTGA
1 TTATCAAAATTTCATAGAGTGA
*
11746 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGAGTGA
11768 TTATCAAAATT
1 TTATCAAAATT
11779 CAATAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:12866 original size:2 final size:2
Alignment explanation
Indices: 12859--12891 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12849 AATTGTCAAC
12859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12892 TAAGAATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13162 original size:51 final size:51
Alignment explanation
Indices: 13106--13208 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
13096 TATTTATGTA
* *
13106 TTTGGTTTGTAGGTAGTTTATTTATGGTATAGTTTCTAGGGTAGGTGATAT
1 TTTGGTTTGTAGGTAGTTTATTTATGGTATAGTTTCTAGGATAGATGATAT
13157 TTTGGTTTGTAGGTAGTTTATTTATGGTATAGTTTCTAGGATAGATGATAT
1 TTTGGTTTGTAGGTAGTTTATTTATGGTATAGTTTCTAGGATAGATGATAT
13208 T
1 T
13209 AGAGATTTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.21, C:0.02, G:0.27, T:0.50
Consensus pattern (51 bp):
TTTGGTTTGTAGGTAGTTTATTTATGGTATAGTTTCTAGGATAGATGATAT
Found at i:13996 original size:15 final size:17
Alignment explanation
Indices: 13976--14008 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
13966 AATTCGGACA
13976 AAAAAATT-T-AATACT
1 AAAAAATTATAAATACT
13991 AAAAAATTATAAATACT
1 AAAAAATTATAAATACT
14008 A
1 A
14009 CGGCTGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAAATTATAAATACT
Found at i:15341 original size:20 final size:20
Alignment explanation
Indices: 15297--15341 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
15287 ATTTTCTTCT
* *
15297 TCTCCATATTCTATTGTCTC
1 TCTCCATATTCAATTCTCTC
15317 TCTCCATACTTCAATTCTCTC
1 TCTCCATA-TTCAATTCTCTC
15338 -CTCC
1 TCTCC
15342 CTTACTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.16, C:0.38, G:0.02, T:0.44
Consensus pattern (20 bp):
TCTCCATATTCAATTCTCTC
Found at i:15836 original size:31 final size:31
Alignment explanation
Indices: 15765--15836 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
15755 GTCTATCAGC
* *
15765 TTTTAATTTGTTTAATTTAAGGCTTTCATTT
1 TTTTAATTTATTTAATTTAAGGCTTTAATTT
* *
15796 TAATT-ATTTATTTAATTTAATGC-TTAATTT
1 T-TTTAATTTATTTAATTTAAGGCTTTAATTT
15826 GTTTTAATTTA
1 -TTTTAATTTA
15837 AGATTGATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 8 0.24
31 23 0.70
32 2 0.06
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (31 bp):
TTTTAATTTATTTAATTTAAGGCTTTAATTT
Found at i:16510 original size:16 final size:16
Alignment explanation
Indices: 16486--16543 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
16476 CTACTTGAGA
16486 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
* *
16502 CCAAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
* *
16518 CCGAGCCCAAAAATAC
1 CCGAACCCGAAAATAC
16534 CCGAACCCGA
1 CCGAACCCGA
16544 TTGAACCCGA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 3 0.09
16 26 0.81
17 3 0.09
ACGTcount: A:0.41, C:0.41, G:0.12, T:0.05
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:16551 original size:16 final size:16
Alignment explanation
Indices: 16532--16573 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
16522 GCCCAAAAAT
*
16532 ACCCGAACCCGATTGA
1 ACCCGAACCCGAATGA
*
16548 ACCCGAACCTGAATGA
1 ACCCGAACCCGAATGA
*
16564 ACCCAAACCC
1 ACCCGAACCC
16574 AAAAAAATCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.40, G:0.14, T:0.10
Consensus pattern (16 bp):
ACCCGAACCCGAATGA
Found at i:16551 original size:32 final size:32
Alignment explanation
Indices: 16486--16556 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
16476 CTACTTGAGA
*
16486 CCGAACCCGAAAATACCCAAACCCGACATAAC
1 CCGAACCCAAAAATACCCAAACCCGACATAAC
* * *
16518 CCGAGCCCAAAAATACCCGAACCCGA-TTGAAC
1 CCGAACCCAAAAATACCCAAACCCGACAT-AAC
16550 CCGAACC
1 CCGAACC
16557 TGAATGAACC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.39, C:0.41, G:0.13, T:0.07
Consensus pattern (32 bp):
CCGAACCCAAAAATACCCAAACCCGACATAAC
Found at i:23706 original size:15 final size:15
Alignment explanation
Indices: 23688--23720 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
23678 GTCTCAAGGG
*
23688 CATGATGGATATGCT
1 CATGATGGATATACT
23703 CATGATGGATATACT
1 CATGATGGATATACT
23718 CAT
1 CAT
23721 CATATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (15 bp):
CATGATGGATATACT
Found at i:25520 original size:29 final size:27
Alignment explanation
Indices: 25483--25545 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
25473 CCATTTTTTT
25483 AAAT-ATATTTCTAA-ATTGCCATTATTA
1 AAATAATATTT-TAATATT-CCATTATTA
25510 AATATAATATTTTAATTATTCCATTATTA
1 AA-ATAATATTTTAA-TATTCCATTATTA
25539 AAATAAT
1 AAATAAT
25546 GGAAATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
27 2 0.06
28 10 0.31
29 17 0.53
30 3 0.09
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (27 bp):
AAATAATATTTTAATATTCCATTATTA
Found at i:28382 original size:22 final size:22
Alignment explanation
Indices: 28248--28415 Score: 100
Period size: 22 Copynumber: 7.7 Consensus size: 22
28238 GACAGAAAGA
*
28248 TTATCAAAA-ATCATAGGA-AG
1 TTATCAAAATTTCATAGGATAG
* *
28268 -GATACAAAATTTCATAGGAAAG
1 TTAT-CAAAATTTCATAGGATAG
* *
28290 TTTATTAAAATTTCATA-GTTAGG
1 -TTATCAAAATTTCATAGGATA-G
* * *
28313 TTACCAAAGTTTCTTATGG--AG
1 TTATCAAAATTTCATA-GGATAG
* * * *
28334 TTTATCACAATTTTATAAG-TAA
1 -TTATCAAAATTTCATAGGATAG
*
28356 TTATCAAAATTTCATATGG-TGG
1 TTATCAAAATTTCATA-GGATAG
*
28378 TTATCAAAATTTAATAGGATAG
1 TTATCAAAATTTCATAGGATAG
28400 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
28416 AAAATATTCA
Statistics
Matches: 111, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.02
20 5 0.05
21 26 0.23
22 63 0.57
23 12 0.11
24 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGATAG
Found at i:28382 original size:43 final size:44
Alignment explanation
Indices: 28317--28415 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 44
28307 GTTAGGTTAC
* * * * *
28317 CAAAGTTTCTTATGGAGTTTATCACAATTTTATAAG-TAATTAT
1 CAAAATTTCATATGGAGGTTATCAAAATTTAATAAGATAATTAT
* * *
28360 CAAAATTTCATATGGTGGTTATCAAAATTTAATAGGATAGTTAT
1 CAAAATTTCATATGGAGGTTATCAAAATTTAATAAGATAATTAT
28404 CAAAATTTCATA
1 CAAAATTTCATA
28416 AAAATATTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 29 0.62
44 18 0.38
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (44 bp):
CAAAATTTCATATGGAGGTTATCAAAATTTAATAAGATAATTAT
Found at i:28489 original size:2 final size:2
Alignment explanation
Indices: 28482--28511 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
28472 AGTTTTGTTA
28482 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28512 AAAGTACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29490 original size:22 final size:22
Alignment explanation
Indices: 29439--29667 Score: 144
Period size: 22 Copynumber: 10.4 Consensus size: 22
29429 AAGGAGTACT
*
29439 AAAATTTGATAGA-AGGTTATC
1 AAAATTTCATAGAGAGGTTATC
* *
29460 -AAATCTCATAGAGTGGTTATC
1 AAAATTTCATAGAGAGGTTATC
* * * *
29481 GAAATTTCATAAAAATCAGATTATC
1 AAAATTTCAT--AGA-GAGGTTATC
*
29506 AAAATTT-ATA-AGAAGATTATC
1 AAAATTTCATAGAG-AGGTTATC
* * ***
29527 AAAATTTTATAGTGTTATTATC
1 AAAATTTCATAGAGAGGTTATC
* *
29549 AAAATTTCAAAGCGAGGTTATC
1 AAAATTTCATAGAGAGGTTATC
* * *
29571 AAAATTACATA-ATGTGATTATC
1 AAAATTTCATAGA-GAGGTTATC
* * *
29593 AAAATTTCATAGAGGGGTCAAC
1 AAAATTTCATAGAGAGGTTATC
* * *
29615 AAAATTTTATAGAGAGTTTATT
1 AAAATTTCATAGAGAGGTTATC
*
29637 AAAATTTCATAAAGAGGTTATC
1 AAAATTTCATAGAGAGGTTATC
*
29659 AAATTTTCA
1 AAAATTTCA
29668 AAATGTGATT
Statistics
Matches: 158, Mismatches: 40, Indels: 19
0.73 0.18 0.09
Matches are distributed among these distances:
20 10 0.06
21 23 0.15
22 107 0.68
23 2 0.01
24 4 0.03
25 12 0.08
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGAGAGGTTATC
Found at i:29591 original size:44 final size:45
Alignment explanation
Indices: 29455--30041 Score: 193
Period size: 44 Copynumber: 13.3 Consensus size: 45
29445 TGATAGAAGG
* * * **
29455 TTATC-AAATCTCAT-AGAGTGGTTATCGAAATTTCATAAAAATCAGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCAT---AATGTGA
* * * *
29501 TTATCAAAATTT-ATAAGA-AGATTATCAAAATTTTATAGTGTTA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* *
29544 TTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * *
29588 TTATCAAAATTTCAT-AGAGGGGTCAACAAAATTTTATAGA-GAGT
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATA-ATGTGA
* * *
29632 TTATTAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * *
29676 TTACCAAAATTTCATAGTGGTATTTTTTGGGAGGTTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATA-----A------GAGAGGTTATCAAAATTTCATAATGTGA
* * * * *
29732 TTA-CCAAA--T--TAGGA-AGGTTATTAAACTTT--TATTGTGGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGT-GA
* * *
29770 GTTATCAAAATTTC---AG-GCAGGATATCAAAATTTCATAGT-TTA
1 -TTATCAAAATTTCATAAGAG-AGGTTATCAAAATTTCATAATGTGA
* *
29812 GTTTTCAAAATTTCATAGGAG-GGTTATCAAAATTTCATAGTATGT-A
1 -TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATA--ATGTGA
* * * * * *
29858 -GATCAAAATTTCAT-AGGGAGATTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * *
29901 TTATTAAAA-TT--T--G-TA-GTTATCAAGATTTCATAAGGAGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * * *
29939 TTATCAAAATTT-TTATAGGGAGATTTGTCAAAATTTTATAGGAAG-GT
1 TTATCAAAATTTCATA-AGAGAG-GTTATCAAAATTTCATA--ATGTGA
* *
29986 TTATCAAAATTTCAT-AGCA-AGGTTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAAG-AGAGGTTATCAAAATTTCATAATGTGA
30030 TTATCAAAATTT
1 TTATCAAAATTT
30042 TAGAGTGTAA
Statistics
Matches: 396, Mismatches: 92, Indels: 108
0.66 0.15 0.18
Matches are distributed among these distances:
37 4 0.01
38 27 0.07
39 19 0.05
40 7 0.02
41 2 0.01
42 30 0.08
43 26 0.07
44 167 0.42
45 16 0.04
46 41 0.10
47 22 0.06
48 3 0.01
49 1 0.00
51 2 0.01
53 1 0.00
55 4 0.01
56 24 0.06
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
Found at i:29641 original size:88 final size:88
Alignment explanation
Indices: 29526--29692 Score: 230
Period size: 88 Copynumber: 1.9 Consensus size: 88
29516 AGAAGATTAT
* * * *
29526 CAAAATTTTATAGTGTTATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTTATAGAGGTATTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
*
29590 ATCAAAATTTCATAGAGGGGTCAA
65 ACCAAAATTTCATAGAGGGGTCAA
* * *
29614 CAAAATTTTATAGAGAGT-TTATTAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATT
1 CAAAATTTTATAGAG-GTATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATT
29678 ACCAAAATTTCATAG
65 ACCAAAATTTCATAG
29693 TGGTATTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
88 66 0.96
89 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (88 bp):
CAAAATTTTATAGAGGTATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCATAGAGGGGTCAA
Found at i:29733 original size:22 final size:21
Alignment explanation
Indices: 29707--30041 Score: 154
Period size: 22 Copynumber: 15.7 Consensus size: 21
29697 ATTTTTTGGG
29707 AGGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
* * *
29728 ATGGTTA-CCAAA-TT-A-GGA
1 A-GGTTATCAAAATTTCATAGT
* * * *
29746 AGGTTATTAAACTTTTATTGT
1 AGGTTATCAAAATTTCATAGT
* * *
29767 GGAGTTATCAAAATTTCA-GGC
1 AG-GTTATCAAAATTTCATAGT
*
29788 AGGATATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG--T
* *
29811 A-GTTTTCAAAATTTCATAGG
1 AGGTTATCAAAATTTCATAGT
29831 AGGGTTATCAAAATTTCATAGT
1 A-GGTTATCAAAATTTCATAGT
* * *
29853 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATA-GT
* * *
29876 AGATTAACAAAATTTCATAAT
1 AGGTTATCAAAATTTCATAGT
*
29897 GAGGTTATTAAAA-TT--T-GT
1 -AGGTTATCAAAATTTCATAGT
* *
29915 A-GTTATCAAGATTTCATAAGG
1 AGGTTATCAAAATTTCAT-AGT
* * *
29936 AGATTATCAAAATTTTTATAGGG
1 AGGTTATCAAAA-TTTCATA-GT
* * * *
29959 AGATTTGTCAAAATTTTATAGGA
1 AG-GTTATCAAAATTTCATA-GT
*
29982 AGGTTTATCAAAATTTCATAGCA
1 AGG-TTATCAAAATTTCATAG-T
*
30005 AGGTTATCACAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
30026 -GTGATTATCAAAATTT
1 AG-G-TTATCAAAATTT
30042 TAGAGTGTAA
Statistics
Matches: 236, Mismatches: 51, Indels: 53
0.69 0.15 0.16
Matches are distributed among these distances:
16 8 0.03
17 8 0.03
18 5 0.02
19 5 0.02
20 19 0.08
21 17 0.07
22 124 0.53
23 42 0.18
24 8 0.03
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGT
Found at i:29975 original size:23 final size:23
Alignment explanation
Indices: 29917--30041 Score: 103
Period size: 23 Copynumber: 5.5 Consensus size: 23
29907 AAATTTGTAG
* *
29917 TTATCAAGATTTCATAAGGAGA-
1 TTATCAAAATTTCATAGGGAGAT
*
29939 TTATCAAAATTTTTATAGGGAGAT
1 TTATCAAAA-TTTCATAGGGAGAT
* * * *
29963 TTGTCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTCATAGGGAGAT
** *
29986 TTATCAAAATTTCATAGCAAG-G
1 TTATCAAAATTTCATAGGGAGAT
* * *
30008 TTATCACAATTTCATAGTGTGA-
1 TTATCAAAATTTCATAGGGAGAT
30030 TTATCAAAATTT
1 TTATCAAAATTT
30042 TAGAGTGTAA
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
22 36 0.42
23 41 0.48
24 8 0.09
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGAT
Found at i:30048 original size:22 final size:22
Alignment explanation
Indices: 30008--30054 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
29998 CATAGCAAGG
* * *
30008 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTAA
*
30030 TTATCAAAATTTTAGAGTGTAA
1 TTATCAAAATTTCAGAGTGTAA
30052 TTA
1 TTA
30055 CTAACAATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTAA
Found at i:30110 original size:22 final size:22
Alignment explanation
Indices: 30085--30144 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
30075 TTTTAAATTT
*
30085 TCATAATGTGGTTATCAATATA
1 TCATAATGTGGTTATCAACATA
* *
30107 TCAT-ATGGAGGTTATCAACATC
1 TCATAAT-GTGGTTATCAACATA
*
30129 TCATAGTGTTGGTTAT
1 TCATAATG-TGGTTAT
30145 TAAAATTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.07
22 21 0.70
23 7 0.23
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (22 bp):
TCATAATGTGGTTATCAACATA
Found at i:30250 original size:22 final size:21
Alignment explanation
Indices: 30212--30252 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
30202 GGAGATTAAC
*
30212 AAAATTTCATAAGAAGGTTTA
1 AAAATTTCATAAAAAGGTTTA
*
30233 AAAATTTTTATAAAAAGGTT
1 AAAA-TTTCATAAAAAGGTT
30253 CTTGAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAATTTCATAAAAAGGTTTA
Found at i:49291 original size:107 final size:109
Alignment explanation
Indices: 49124--49364 Score: 299
Period size: 107 Copynumber: 2.2 Consensus size: 109
49114 GGGTTTCAAA
* ** * * *
49124 ATTTGAGATTTACCCTTTTAAAAAATAAAACAATTTTATAAATGGGGCTAAATCTTATTTATAAG
1 ATTTAAGATTTACCCTTAAAAAAAATAAAACAATTTTATAAATGGAGCTAAACCTTATTTAAAAG
*
49189 TGTTCAAACTTATTTTTCTAGAACCCTAAGATAGTGGATTTTTC
66 TGTTCAAACTTATTTTTCTAAAACCCTAAGATAGTGGATTTTTC
*
49233 ATTTAAGATTTA-CCTTAAAAAAAATAAAAC-ATATTT-TAATTGGAGCTAAACCTTATTTAAAA
1 ATTTAAGATTTACCCTTAAAAAAAATAAAACAAT-TTTATAAATGGAGCTAAACCTTATTTAAAA
* * * * ***
49295 GTGTTCAAACTTATTTTTCTAAAATCCTAAAATAATGGGTCTTAAA
65 GTGTTCAAACTTATTTTTCTAAAACCCTAAGATAGTGGAT-TTTTC
*
49341 ATTTAAAATTTACCCTTAAAAAAA
1 ATTTAAGATTTACCCTTAAAAAAA
49365 TATTTATAAT
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
107 59 0.52
108 32 0.28
109 22 0.19
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (109 bp):
ATTTAAGATTTACCCTTAAAAAAAATAAAACAATTTTATAAATGGAGCTAAACCTTATTTAAAAG
TGTTCAAACTTATTTTTCTAAAACCCTAAGATAGTGGATTTTTC
Found at i:63311 original size:26 final size:26
Alignment explanation
Indices: 63282--63331 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
63272 GTAGTCAATT
63282 TTCTAATTTAAAATTGA-TTAAAAAAA
1 TTCTAATTTAAAATT-ACTTAAAAAAA
*
63308 TTCTTATTTAAAATTACTTAAAAA
1 TTCTAATTTAAAATTACTTAAAAA
63332 GCTATATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (26 bp):
TTCTAATTTAAAATTACTTAAAAAAA
Done.