Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold504
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: 117106
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 3476 characters in sequence are not A, C, G, or T
Found at i:38 original size:21 final size:21
Alignment explanation
Indices: 1--444 Score: 482
Period size: 21 Copynumber: 21.1 Consensus size: 21
1 TTTTTAAGTTAAGGGTTTAGGG
1 TTTTTAAGTTAA-GGTTTAGGG
*
23 TTTTTAAGTTAAGGTTTAGAG
1 TTTTTAAGTTAAGGTTTAGGG
* * *
44 TTATTAAATTAAGGTTTAAGG
1 TTTTTAAGTTAAGGTTTAGGG
* *
65 TTTTTAATTTAAGGGTTAGGG
1 TTTTTAAGTTAAGGTTTAGGG
*
86 TTTTTAAGTTAATAG-TTAGGG
1 TTTTTAAGTTAA-GGTTTAGGG
*
107 TTTTTAATTTAAGGTTTAGGG
1 TTTTTAAGTTAAGGTTTAGGG
* * *
128 TCTTTAATTTAAGGGTTAGGG
1 TTTTTAAGTTAAGGTTTAGGG
* **
149 TTTTTAA-TTAAGGGTTATTG
1 TTTTTAAGTTAAGGTTTAGGG
* *
169 TTTTTAAGTTAAGGGTTACGG
1 TTTTTAAGTTAAGGTTTAGGG
*
190 TTTTTCAGTTAAGGTTTAGGG
1 TTTTTAAGTTAAGGTTTAGGG
* * *
211 TTTTTAATTTAAGGGTTAGTG
1 TTTTTAAGTTAAGGTTTAGGG
*
232 TTTTTAAATTAAGGCTTTAGGG
1 TTTTTAAGTTAAGG-TTTAGGG
254 -TTTTAAGTTAAGGTTTAGGG
1 TTTTTAAGTTAAGGTTTAGGG
* *
274 TTATTAAGTTAATGTTTAGGG
1 TTTTTAAGTTAAGGTTTAGGG
* * * *
295 ATTTTAATTTAAGGGTTAGGA
1 TTTTTAAGTTAAGGTTTAGGG
* * *
316 TTTTTAAGTTTAGGGTTAGGA
1 TTTTTAAGTTAAGGTTTAGGG
*
337 TTTTTAAGGTAAGGGTTTAGGG
1 TTTTTAAGTTAA-GGTTTAGGG
* *
359 ATTTCAAGTTAAGGTTTAGGG
1 TTTTTAAGTTAAGGTTTAGGG
* *
380 TTATTACGTTAAGGTTTAGGG
1 TTTTTAAGTTAAGGTTTAGGG
*
401 TTTTTAA-TTAAGGGTTAGGG
1 TTTTTAAGTTAAGGTTTAGGG
*
421 TTTTTAAGTTAATAGTTTAGGG
1 TTTTTAAGTTAA-GGTTTAGGG
443 TT
1 TT
445 AGGGTTTTTT
Statistics
Matches: 356, Mismatches: 58, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
20 45 0.13
21 268 0.75
22 43 0.12
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.46
Consensus pattern (21 bp):
TTTTTAAGTTAAGGTTTAGGG
Found at i:465 original size:27 final size:28
Alignment explanation
Indices: 411--471 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
401 TTTTTAATTA
*
411 AGGGTTAGGGTTTTTAAGTTAATAGTTT
1 AGGGTTAGGGTTTTTAAGTTAAGAGTTT
* *
439 AGGGTTAGGGTTTTT-TGTTAAGGGTTT
1 AGGGTTAGGGTTTTTAAGTTAAGAGTTT
*
466 AAGGTT
1 AGGGTT
472 GGTCAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (28 bp):
AGGGTTAGGGTTTTTAAGTTAAGAGTTT
Found at i:723 original size:17 final size:16
Alignment explanation
Indices: 684--764 Score: 67
Period size: 17 Copynumber: 4.8 Consensus size: 16
674 GTAATTGTAA
684 AAAATTA-T-ATTTAT
1 AAAATTATTAATTTAT
698 AAAATTATTAATTTAT
1 AAAATTATTAATTTAT
*
714 AAATTGTATTAATGGTTAGT
1 AAAAT-TATTAAT--TTA-T
*
734 AAAATTATCAAATTATAT
1 AAAATTAT-TAATT-TAT
*
752 CAAATTATTAATT
1 AAAATTATTAATT
765 GTTAGTACCT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
14 7 0.13
15 1 0.02
16 10 0.19
17 11 0.20
18 9 0.17
19 8 0.15
20 8 0.15
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (16 bp):
AAAATTATTAATTTAT
Found at i:915 original size:114 final size:114
Alignment explanation
Indices: 697--1069 Score: 507
Period size: 114 Copynumber: 3.4 Consensus size: 114
687 ATTATATTTA
* *
697 TAAAATTATTAATTTATAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTA
1 TAAAATTATTAACTGAT-AATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTA
* * * *
762 ATTGTTAGTACCTGTCAAAACATTTTTCCAGGA-CTAACATTTTTTGAATG
65 ATTGTTAGTACCAGTCAAAACATTTTTCCA-AATCTAACATTATGTGAATG
*
812 TAGAATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAA
1 TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAA
* * * * *
877 TTGTTAGTACGAGTCAGAACATTTTTCCAAATTTAACATTGTGTGAATT
66 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATG
926 TAAAATTATTAACTGATAATTGTATTAATGGTTAG------TA--AAA-T-TATCAAATTATTAA
1 TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAA
* * * *
981 TTGTTAGTGCCAGTCAAAAAAATTTTCCAAATCTAACATTATGTGACTG
66 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATG
1030 TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAA
1 TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAA
1070 ACCTTAAGGT
Statistics
Matches: 231, Mismatches: 21, Indels: 18
0.86 0.08 0.07
Matches are distributed among these distances:
104 89 0.39
105 1 0.00
106 3 0.01
108 2 0.01
113 1 0.00
114 121 0.52
115 14 0.06
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (114 bp):
TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAA
TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATG
Found at i:996 original size:104 final size:104
Alignment explanation
Indices: 863--1069 Score: 333
Period size: 104 Copynumber: 2.0 Consensus size: 104
853 TATCAAATTA
* * * * * * *
863 TATCAAATTATTAATTGTTAGTACGAGTCAGAACATTTTTCCAAATTTAACATTGTGTGAATTTA
1 TATCAAATTATTAATTGTTAGTACCAGTCAAAAAAATTTTCCAAATCTAACATTATGTGAATGTA
928 AAATTATTAACTGATAATTGTATTAATGGTTAGTAAAAT
66 AAATTATTAACTGATAATTGTATTAATGGTTAGTAAAAT
* *
967 TATCAAATTATTAATTGTTAGTGCCAGTCAAAAAAATTTTCCAAATCTAACATTATGTGACTGTA
1 TATCAAATTATTAATTGTTAGTACCAGTCAAAAAAATTTTCCAAATCTAACATTATGTGAATGTA
1032 AAATTATTAACTGATAATTGTATTAATGGTTAGTAAAA
66 AAATTATTAACTGATAATTGTATTAATGGTTAGTAAAA
1070 ACCTTAAGGT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 94 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (104 bp):
TATCAAATTATTAATTGTTAGTACCAGTCAAAAAAATTTTCCAAATCTAACATTATGTGAATGTA
AAATTATTAACTGATAATTGTATTAATGGTTAGTAAAAT
Found at i:1823 original size:21 final size:21
Alignment explanation
Indices: 1077--1802 Score: 718
Period size: 21 Copynumber: 34.2 Consensus size: 21
1067 AAAACCTTAA
**
1077 GGTTTTTAAGTTAATGATTTAG
1 GGTTTTTAAGTTAA-GGGTTAG
1099 GG-TTTTAAGTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
* * **
1119 GGTTATTAAGCTAAGATTTAG
1 GGTTTTTAAGTTAAGGGTTAG
* *
1140 GTTTTTTAATTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
1161 GGTTTTTAAGTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
* *
1182 GGTTTTTAATTTAATGGTTAGGTTTAC
1 GGTTTTTAAGTTAA--G---GG-TTAG
*
1209 GGTTTTTAAGTTAAAGGTTTAG
1 GGTTTTTAAGTT-AAGGGTTAG
* *
1231 GGTATAATTGT-A-TTAATGGTTTAA
1 GGT-T--TT-TAAGTTAA-GGGTTAG
*
1255 GGTTTTTAATTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
1276 GGTTTTTAA-TTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
1296 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGG-TTAG
* *
1318 GGTTTTTAAGTTAAGGTTTTG
1 GGTTTTTAAGTTAAGGGTTAG
*
1339 GGTTTTTAATTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
* *
1360 AGTTTTTAAGTTAAGGGTTAA
1 GGTTTTTAAGTTAAGGGTTAG
* *
1381 GGTTTTTAAGTTATTGGTTTAG
1 GGTTTTTAAGTTA-AGGGTTAG
* *
1403 TGTATTTAAGTTAA-GGTTAAG
1 GGTTTTTAAGTTAAGGGTT-AG
** *
1424 GGTTACTAAGTTAAGGTTTAG
1 GGTTTTTAAGTTAAGGGTTAG
* * *
1445 GATTTTTAATTTAAGGGTTTG
1 GGTTTTTAAGTTAAGGGTTAG
*
1466 GG-TTTTAAGTTAAGGGTTTG
1 GGTTTTTAAGTTAAGGGTTAG
* *
1486 AGTTTTTAATTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
1507 GGTTTTTAA-TTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
*
1527 GGTTTTTAAGTTATGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
*
1548 GGTTTTTAATTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGG-TTAG
* * *
1570 GG-TTTTAAGTGAAGGTTTAA
1 GGTTTTTAAGTTAAGGGTTAG
* *
1590 GGTTATTAAGTTAAGGTTTAG
1 GGTTTTTAAGTTAAGGGTTAG
* *
1611 GGCTTTTAATTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
*
1632 GATTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAGGG-TTAG
*
1654 GG-TTTTAAGTTAAGGTTTAG
1 GGTTTTTAAGTTAAGGGTTAG
** *
1674 GGTAATTAAGTTAAGGTTTAG
1 GGTTTTTAAGTTAAGGGTTAG
* *
1695 GGTTTTTAATTTAAGGGCTAG
1 GGTTTTTAAGTTAAGGGTTAG
*
1716 GGTTTTTAAGTTAA-GGTTTG
1 GGTTTTTAAGTTAAGGGTTAG
* *
1736 GAGTTTTAAATTTAAGGGTTAG
1 G-GTTTTTAAGTTAAGGGTTAG
*
1758 GATTTTTAA-TTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
* *
1778 GATTTTGAAGTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGGTTAG
1799 GGTT
1 GGTT
1803 AGGGTTTTTT
Statistics
Matches: 584, Mismatches: 91, Indels: 59
0.80 0.12 0.08
Matches are distributed among these distances:
20 104 0.18
21 372 0.64
22 68 0.12
23 6 0.01
24 11 0.02
25 3 0.01
26 4 0.01
27 14 0.02
28 2 0.00
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.45
Consensus pattern (21 bp):
GGTTTTTAAGTTAAGGGTTAG
Found at i:2286 original size:114 final size:114
Alignment explanation
Indices: 2062--2332 Score: 452
Period size: 114 Copynumber: 2.4 Consensus size: 114
2052 AAATTATATT
* * * * *
2062 TGTAAAATTATTAATTGATAAATTGTATTAATGGTGAGTAAAATTATCAAATTATATCAAATTTT
1 TGTAAAATTATTAACTAAT-AATCGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTAT
*
2127 TAATTGTTAGTGCCAGTCAAAACATTTTTCCAAATCTAACTTTATGTGAA
65 TAATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACTTTATGTGAA
* *
2177 TGTAAAATTATTAACTAATAATCGTATTAATGGTTAGTAAAATTATCGAATTATATCTAATTATT
1 TGTAAAATTATTAACTAATAATCGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATT
*
2242 AATTGTTAGTACTAGTCAAAACATTTTTCCAAATCTAACTTTATGTGAA
66 AATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACTTTATGTGAA
2291 TGTAAAATTATTAACTAATAATCGTATTAATGGTTAGTAAAA
1 TGTAAAATTATTAACTAATAATCGTATTAATGGTTAGTAAAA
2333 AACTTAAGGG
Statistics
Matches: 147, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
114 130 0.88
115 17 0.12
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (114 bp):
TGTAAAATTATTAACTAATAATCGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATT
AATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACTTTATGTGAA
Found at i:2429 original size:20 final size:21
Alignment explanation
Indices: 2339--3695 Score: 1059
Period size: 21 Copynumber: 63.0 Consensus size: 21
2329 AAAAAACTTA
2339 AGGG-TTTTAAGTTAAGGGTTT
1 AGGGTTTTTAAGTTAAGGG-TT
*
2360 AGGGTGTTTTAAGTTAAGGTTTT
1 AGGGT-TTTTAAGTTAAGG-GTT
2383 AGGGTTTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
2404 AGGGTTTTTAATTTAATGGTTAGGTTT
1 AGGGTTTTTAAGTTAA--G---GG-TT
* *
2431 ACGGTTTTTAAGTTAAAGGTTT
1 AGGGTTTTTAAGTT-AAGGGTT
*
2453 AGGGTATAATTGT-A-TTAATGGTT
1 AGGGT-T--TT-TAAGTTAAGGGTT
* * *
2476 ---TTTTTTAA-TTTAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
2493 AAGGTTTTTAATTTAATGGTTAGGGTT
1 AGGGTTTTTAAGTT-A-----AGGGTT
* *
2520 AGGGTTTTTAAGGTAAAGGTTT
1 AGGGTTTTTAA-GTTAAGGGTT
*
2542 ATGGTTTTTAAGTTAAGGGTTT
1 AGGGTTTTTAAGTTAAGGG-TT
* * *
2564 AGGGTTATTAATTTAAGGGTG
1 AGGGTTTTTAAGTTAAGGGTT
* *
2585 AGGGTTTTTAATTTAATGGTTT
1 AGGGTTTTTAAGTTAA-GGGTT
*
2607 AGGGTTTTTAAGTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* * *
2628 AGAGTTTTTAATTTATGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
2649 AGAGTTTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
2670 AGGGTTTTTAATTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
2691 AGGGTTTTTAATTTAATGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
2712 AGGGTTTGGGATTTTAAGTTTAAGGTTT
1 AGGG--T----TTTTAAG-TTAAGGGTT
2740 AGGGTATAATTGT-A-TTAAGGGTTT
1 AGGGT-T--TT-TAAGTTAAGGG-TT
* * *
2764 AAGATTTTTAATTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
2785 AGGGTTTTTAA-TTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
2805 AGGTTTTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
2826 AGGGTTTTTAAGTTAAGTGTTT
1 AGGGTTTTTAAGTTAAG-GGTT
* *
2848 AGAGTTTTTAAGTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* * **
2869 AGGGTTTTAAATTTAAGATTT
1 AGGGTTTTTAAGTTAAGGGTT
*
2890 AGTGTTTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
2911 AGGGTTTTTAAGTTAAAGGTTT
1 AGGGTTTTTAAGTT-AAGGGTT
* *
2933 AGGGTTTTTGAGTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* * *
2954 AGAGTTATTAAGTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
2975 AAGGTTTTTAATTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
2996 AAGGTTTTTAAGTTAATGGTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
3017 AGGGTTTTTAATTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3038 AGGGTTTTTAATTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3059 AGGGTTTTTAA-TTTAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
** * *
3079 ATTGTTCTTAAGTTAAGAGTT
1 AGGGTTTTTAAGTTAAGGGTT
* * * *
3100 ACGATTTTTCAGTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3121 AGGATTTTT-AGTTTAAGGGTT
1 AGGGTTTTTAAG-TTAAGGGTT
* * *
3142 AGAGTTTTTAATTTAAAGGTT
1 AGGGTTTTTAAGTTAAGGGTT
3163 AGGGTTTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
3184 AGGGTTTTTAAGTTAAGGGTTT
1 AGGGTTTTTAAGTTAAGGG-TT
* *
3206 A-GGATTTTAAGTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* * *
3226 AGGGTTATTAAGCTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3247 AGGGTTTTTAATTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3268 AGGATTTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
3289 AGGGTTTTTAAGTTAAGGGTTT
1 AGGGTTTTTAAGTTAAGGG-TT
* *
3311 AGGGTTTTTAAGTTTAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* * **
3332 AGGGTTATTAATTTAAGATTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
3353 AAGGTTTTTAATTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3374 AAGGTTTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
3395 AGGGTTTTTAATTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
3416 AGGGTTTTTAATTTTAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3437 AGGGTTTCTAA-TTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3457 AGGGTTTTT-TGTTAAGGGTTT
1 AGGGTTTTTAAGTTAAGGG-TT
* * *
3478 AAGGTTTGTCAA-TTAA--ATT
1 AGGGTTT-TTAAGTTAAGGGTT
*** * ***
3497 ATATATTTAACTATAAATTATAAATTT
1 A-GGGTTT---T-TAAGTTA-AGGGTT
*** *
3524 ATAAATTTTTAA--TAAGTCAAGGGTTT
1 A-GGGTTTTTAAGTTAAG----GGT--T
* *
3550 AGGGTTTTTAATTTATGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
3571 AGGGTTTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
3592 -GGAGTTTTTAAGTTAAGGGTTT
1 AGG-GTTTTTAAGTTAAGGG-TT
*
3614 AGGGTTTTTAAGTTAAGGTTT
1 AGGGTTTTTAAGTTAAGGGTT
* *
3635 AAGGTTTTTAATTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3656 AGGG-TTTTAATTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
*
3676 AAGG-TTTTAAGTTAAGGGTT
1 AGGGTTTTTAAGTTAAGGGTT
3696 TCTCAAAAAA
Statistics
Matches: 1100, Mismatches: 163, Indels: 147
0.78 0.12 0.10
Matches are distributed among these distances:
16 1 0.00
17 9 0.01
19 4 0.00
20 113 0.10
21 670 0.61
22 161 0.15
23 47 0.04
24 11 0.01
25 14 0.01
26 8 0.01
27 48 0.04
28 14 0.01
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.47
Consensus pattern (21 bp):
AGGGTTTTTAAGTTAAGGGTT
Found at i:2540 original size:27 final size:27
Alignment explanation
Indices: 2485--2540 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
2475 TTTTTTTAAT
* ** *
2485 TTAGGTTTAAGGTTTTTAATTTAATGG
1 TTAGGGTTAAGGTTTTTAAGGTAAAGG
*
2512 TTAGGGTTAGGGTTTTTAAGGTAAAGG
1 TTAGGGTTAAGGTTTTTAAGGTAAAGG
2539 TT
1 TT
2541 TATGGTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (27 bp):
TTAGGGTTAAGGTTTTTAAGGTAAAGG
Found at i:2726 original size:28 final size:28
Alignment explanation
Indices: 2681--2744 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
2671 GGGTTTTTAA
*
2681 TTTAAGGTTTAGGGTTTTTAA-TTTAATGG
1 TTTAGGGTTTAGGG-TTTTAAGTTTAA-GG
2710 -TTAGGGTTT-GGGATTTTAAGTTTAAGG
1 TTTAGGGTTTAGGG-TTTTAAGTTTAAGG
2737 TTTAGGGT
1 TTTAGGGT
2745 ATAATTGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 11 0.35
28 20 0.65
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (28 bp):
TTTAGGGTTTAGGGTTTTAAGTTTAAGG
Found at i:3853 original size:21 final size:20
Alignment explanation
Indices: 3829--3875 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
3819 CTTTGTCCAG
3829 CTTCTGGCGGCAG-TTCTGGTT
1 CTTCT-GCGG-AGATTCTGGTT
*
3850 CTTCCTGCGGGGATTCTGGTT
1 CTT-CTGCGGAGATTCTGGTT
3871 CTTCT
1 CTTCT
3876 AGTAGGGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 18 0.78
22 2 0.09
ACGTcount: A:0.04, C:0.26, G:0.30, T:0.40
Consensus pattern (20 bp):
CTTCTGCGGAGATTCTGGTT
Found at i:5392 original size:15 final size:15
Alignment explanation
Indices: 5374--5408 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5364 TACAAATGCC
5374 ACAATAATAAATACA
1 ACAATAATAAATACA
5389 ACAATAATAAATACA
1 ACAATAATAAATACA
*
5404 TCAAT
1 ACAAT
5409 GGCATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (15 bp):
ACAATAATAAATACA
Found at i:7383 original size:50 final size:50
Alignment explanation
Indices: 7308--7418 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 50
7298 CTAAGTTTTT
* ** ** *
7308 AATCTGCTCCACTGCAACTTCAGGG-AGATAAGATTTGCCGTCGTGGCTTC
1 AATCTGCTCCACTACAACGCCAGGGAAG-TAAGATTCACCGTCATGGCTTC
* * *
7358 AATCTGCTCCGCTACAACGCCAGGGAAGTAAGATTCACTGTCATGGTTTC
1 AATCTGCTCCACTACAACGCCAGGGAAGTAAGATTCACCGTCATGGCTTC
7408 AATCTGCTCCA
1 AATCTGCTCCA
7419 TTGTAATGCT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 48 0.96
51 2 0.04
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
AATCTGCTCCACTACAACGCCAGGGAAGTAAGATTCACCGTCATGGCTTC
Found at i:7557 original size:50 final size:50
Alignment explanation
Indices: 7503--7686 Score: 145
Period size: 50 Copynumber: 3.7 Consensus size: 50
7493 GCTAGGGAGA
* * *
7503 TAAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTTCAATGCCAGGGAAG
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCACTTCAATGTCAGGGAAG
* * * * * ** * * * *
7553 TAAGACTCACCGCCGCGGCTTCAGTCT-TTTAAATTGCAATGTTAAGGAAA
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCACTT-CAATGTCAGGGAAG
* * * * * ** *
7603 CAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGTCAGGGGAG
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCACTTCAATGTCAGGGAAG
*
7653 TAAGATTCACCGTCGTGGTTTCAATCTGCTCCAC
1 TAAGATTCACCGTCGTGGCTTCAATCTGCTCCAC
7687 CGTAATACTA
Statistics
Matches: 96, Mismatches: 36, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
49 3 0.03
50 89 0.93
51 4 0.04
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
TAAGATTCACCGTCGTGGCTTCAATCTGCTCCACTTCAATGTCAGGGAAG
Found at i:7858 original size:267 final size:267
Alignment explanation
Indices: 7337--7866 Score: 754
Period size: 267 Copynumber: 2.0 Consensus size: 267
7327 TCAGGGAGAT
* * * *
7337 AAGATTTGCCGTCGTGGCTTCAATCTGCTCCGCTACAACGCCAGGGAAGTAAGATTCACTGTCAT
1 AAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAGATTCACCGTCAT
** * *
7402 GGTTTCAATCTGCTCCATTGTAATGCTAAAGAGATAGAATTCGCTGCCCACAGCTTTAATCCTCT
66 GGTTTCAATCTGCTCCACCGTAATACTAAAGAGATAGAATTCGCTGCCCACAGCTTTAATCCACT
* *
7467 CCACTTCAACTAATCCAAGCCTTAACGCTAGGGAGATAAGATTCGCCGTCGTGGCTTCAATCTGC
131 CCACTTCAACTAATCCAAGCCTTAACACTAGAGAGATAAGATTCGCCGTCGTGGCTTCAATCTGC
* * * * *
7532 TCCGCTTCAATGCCAGGGAAGTAAGACTCACCGCCGCGGCTTCAGTCTTTTAAATTGCAATGTTA
196 TCCGCTACAATGCCAGGGAAATAAGACTCACCGCCGCGGCTTCAATATTTTAAATTGCAATGTCA
7597 AGGAAAC
261 AGGAAAC
* * * * *
7604 AAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGTCAGGGGAGTAAGATTCACCGTCGT
1 AAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAGATTCACCGTCAT
* *
7669 GGTTTCAATCTGCTCCACCGTAATACTAACGAGATAGGATTCGCTGCCCACAGCTTTAATCCACT
66 GGTTTCAATCTGCTCCACCGTAATACTAAAGAGATAGAATTCGCTGCCCACAGCTTTAATCCACT
* * *
7734 CCACTTCAGCTAATCCAAGCCTTAATACTAGAGAGATAAGATTCGCCGTTGTGGCTTCAATCTGC
131 CCACTTCAACTAATCCAAGCCTTAACACTAGAGAGATAAGATTCGCCGTCGTGGCTTCAATCTGC
* * * ** * * **
7799 TCCGCTACAATGCCATGGAAATAAGATTCGCCGTTGTGGTTTCAATATTTTCCATTGCAATGTCA
196 TCCGCTACAATGCCAGGGAAATAAGACTCACCGCCGCGGCTTCAATATTTTAAATTGCAATGTCA
7864 AGG
261 AGG
7867 CGATAAGACT
Statistics
Matches: 229, Mismatches: 34, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
267 229 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (267 bp):
AAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAGATTCACCGTCAT
GGTTTCAATCTGCTCCACCGTAATACTAAAGAGATAGAATTCGCTGCCCACAGCTTTAATCCACT
CCACTTCAACTAATCCAAGCCTTAACACTAGAGAGATAAGATTCGCCGTCGTGGCTTCAATCTGC
TCCGCTACAATGCCAGGGAAATAAGACTCACCGCCGCGGCTTCAATATTTTAAATTGCAATGTCA
AGGAAAC
Found at i:7873 original size:50 final size:50
Alignment explanation
Indices: 7766--7874 Score: 119
Period size: 50 Copynumber: 2.2 Consensus size: 50
7756 TAATACTAGA
* * *
7766 GAGATAAGATTCGCCGTTGTGGCTTCAATCTGCTCCGCTACAATGCCATG
1 GAGATAAGATTCGCCGTTGTGGCTTCAATATGCTCCACTACAATGCCAAG
* * ** * * *
7816 GAAATAAGATTCGCCGTTGTGGTTTCAATATTTTCCATTGCAATGTCAAG
1 GAGATAAGATTCGCCGTTGTGGCTTCAATATGCTCCACTACAATGCCAAG
*
7866 GCGATAAGA
1 GAGATAAGA
7875 CTAAATATCT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (50 bp):
GAGATAAGATTCGCCGTTGTGGCTTCAATATGCTCCACTACAATGCCAAG
Found at i:19818 original size:15 final size:15
Alignment explanation
Indices: 19800--19834 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
19790 TACAAATGCC
19800 ACAATAATAAATACA
1 ACAATAATAAATACA
19815 ACAATAATAAATACA
1 ACAATAATAAATACA
*
19830 TCAAT
1 ACAAT
19835 GGCATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (15 bp):
ACAATAATAAATACA
Found at i:19935 original size:25 final size:26
Alignment explanation
Indices: 19897--19945 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
19887 CATGACATGC
**
19897 AAAATATTAAATGAATGAAATATAGA
1 AAAATATTAAATGAAAAAAATATAGA
*
19923 AAAATATT-CATGAAAAAAATATA
1 AAAATATTAAATGAAAAAAATATA
19946 AATATATACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (26 bp):
AAAATATTAAATGAAAAAAATATAGA
Found at i:21678 original size:20 final size:20
Alignment explanation
Indices: 21641--21678 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21631 TTTATTTCTA
*
21641 AAAATCTACATAATAATTAT
1 AAAATCTACATAAAAATTAT
21661 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
21679 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTAT
Found at i:22680 original size:11 final size:11
Alignment explanation
Indices: 22666--22729 Score: 85
Period size: 11 Copynumber: 5.7 Consensus size: 11
22656 TTAAATATGG
*
22666 ATTTGAGAGAA
1 ATTTGAGAGGA
22677 ATTTG-GAAGGA
1 ATTTGAG-AGGA
22688 ATTTGAGAGGA
1 ATTTGAGAGGA
22699 ATTTGAGAGGA
1 ATTTGAGAGGA
*
22710 ATTTGAGAGAAA
1 ATTTGAGAG-GA
22722 ATTTGAGA
1 ATTTGAGA
22730 TAGGATTAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
10 1 0.02
11 37 0.77
12 10 0.21
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (11 bp):
ATTTGAGAGGA
Found at i:26276 original size:17 final size:16
Alignment explanation
Indices: 26254--26287 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26244 TTTTAAATAA
26254 TTTTATATATATAATTT
1 TTTTATAT-TATAATTT
*
26271 TTTTATATTATTATTT
1 TTTTATATTATAATTT
26287 T
1 T
26288 GAAATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATATTATAATTT
Found at i:27051 original size:18 final size:18
Alignment explanation
Indices: 27025--27080 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
27015 TCAATGTAAA
*
27025 ATAATTTTAATTTTTTTT
1 ATAAATTTAATTTTTTTT
* *
27043 ATAAATTT-ATATATTGTT
1 ATAAATTTAAT-TTTTTTT
* *
27061 AAAAATTTACTTTTTTTT
1 ATAAATTTAATTTTTTTT
27079 AT
1 AT
27081 TAGGTATTAC
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
17 2 0.07
18 25 0.89
19 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
ATAAATTTAATTTTTTTT
Found at i:42504 original size:3 final size:3
Alignment explanation
Indices: 42498--42531 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42488 TTTTTTTGGT
42498 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
42532 GTACAGGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52175 original size:46 final size:47
Alignment explanation
Indices: 52087--52176 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 47
52077 ACCCTTATAT
* * * *
52087 TAGGAGGTAAATCATATTTTATTCTTTTTATTCAAAAATAGGCATAC
1 TAGGAGGTAAATCACATTTTACTCTCTTCATTCAAAAATAGGCATAC
52134 TAGGAGGTAAATCACA-TTTACTCTCTTCATTCAAAAATAGGCA
1 TAGGAGGTAAATCACATTTTACTCTCTTCATTCAAAAATAGGCA
52177 AATTAATCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 24 0.62
47 15 0.38
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (47 bp):
TAGGAGGTAAATCACATTTTACTCTCTTCATTCAAAAATAGGCATAC
Found at i:54015 original size:2 final size:2
Alignment explanation
Indices: 54002--54041 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
53992 CCTTCTTTCT
* *
54002 TA TA TT TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54042 CATGCAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55403 original size:54 final size:54
Alignment explanation
Indices: 55345--55452 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
55335 TATATATTCA
55345 TAAAAGAGATAGTATTAATTTTAAAATATTGAATTAACTATCATTATAGTTTAG
1 TAAAAGAGATAGTATTAATTTTAAAATATTGAATTAACTATCATTATAGTTTAG
* *
55399 TAAAAGAGATATTATTAATTTTAAAATATTGAATTAATTATCATTATAGTTTAG
1 TAAAAGAGATAGTATTAATTTTAAAATATTGAATTAACTATCATTATAGTTTAG
55453 GGTTTAAGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (54 bp):
TAAAAGAGATAGTATTAATTTTAAAATATTGAATTAACTATCATTATAGTTTAG
Found at i:55507 original size:15 final size:15
Alignment explanation
Indices: 55483--55516 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
55473 CTATCTTAAG
*
55483 GTTTATGGATTATGA
1 GTTTAGGGATTATGA
55498 GTTTAGGGATTATGA
1 GTTTAGGGATTATGA
55513 -TTTA
1 GTTTA
55517 TGGTTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (15 bp):
GTTTAGGGATTATGA
Found at i:55535 original size:14 final size:14
Alignment explanation
Indices: 55521--55585 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
55511 GATTTATGGT
55521 TTAAGGGTT-GGGG
1 TTAAGGGTTAGGGG
* *
55534 TTTAAGGTTTAGTGG
1 -TTAAGGGTTAGGGG
*
55549 TTAGGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
55563 TTAAGGGTTAAGGG
1 TTAAGGGTTAGGGG
*
55577 TTAGGGGTT
1 TTAAGGGTT
55586 TATGATTTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 39 0.93
15 3 0.07
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:55537 original size:21 final size:22
Alignment explanation
Indices: 55513--55578 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
55503 GGGATTATGA
*
55513 TTTATGGTTTAAGGGTT-GGGG
1 TTTAAGGTTTAAGGGTTAGGGG
55534 TTTAAGGTTT-AGTGGTTAGGGG
1 TTTAAGGTTTAAG-GGTTAGGGG
* * *
55556 -TTAGGGGTTAAGGGTTAAGGG
1 TTTAAGGTTTAAGGGTTAGGGG
55577 TT
1 TT
55579 AGGGGTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.05
21 28 0.76
22 7 0.19
ACGTcount: A:0.18, C:0.00, G:0.42, T:0.39
Consensus pattern (22 bp):
TTTAAGGTTTAAGGGTTAGGGG
Found at i:55552 original size:7 final size:7
Alignment explanation
Indices: 55542--55614 Score: 65
Period size: 7 Copynumber: 10.3 Consensus size: 7
55532 GGTTTAAGGT
*
55542 TTAGTGG
1 TTAGGGG
55549 TTAGGGG
1 TTAGGGG
55556 TTAGGGG
1 TTAGGGG
*
55563 TTAAGGG
1 TTAGGGG
*
55570 TTAAGGG
1 TTAGGGG
55577 TTAGGGG
1 TTAGGGG
* **
55584 TTTATGAT
1 -TTAGGGG
* *
55592 TTATGGT
1 TTAGGGG
55599 TTAGGGG
1 TTAGGGG
55606 TTAGGGG
1 TTAGGGG
55613 TT
1 TT
55615 TAGATTAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
7 52 0.93
8 4 0.07
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (7 bp):
TTAGGGG
Found at i:55556 original size:28 final size:27
Alignment explanation
Indices: 55525--55614 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
55515 TATGGTTTAA
55525 GGGTTGGGGTTTAAGGTTTAGTGGTTAG
1 GGGTTGGGGTTTAAGGTTTAG-GGTTAG
*
55553 GGGTTAGGGG-TTAAGGGTTAAGGGTTAG
1 GGGTT-GGGGTTTAA-GGTTTAGGGTTAG
** * *
55581 GGGTTTATGATTTATGGTTTAGGGGTTAG
1 GGG-TTGGGGTTTAAGGTTTA-GGGTTAG
55610 GGGTT
1 GGGTT
55615 TAGATTAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
28 26 0.51
29 25 0.49
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.38
Consensus pattern (27 bp):
GGGTTGGGGTTTAAGGTTTAGGGTTAG
Found at i:55620 original size:28 final size:29
Alignment explanation
Indices: 55534--55617 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
55524 AGGGTTGGGG
* *
55534 TTTAAGGTTTAGTGGTTAGGGG-TTAGGG
1 TTTAAGGTTTAGGGGTTAGGGGTTTAGGA
* * * *
55562 GTTAAGGGTTAAGGGTTAGGGGTTTATGA
1 TTTAAGGTTTAGGGGTTAGGGGTTTAGGA
*
55591 TTTATGGTTTAGGGGTTAGGGGTTTAG
1 TTTAAGGTTTAGGGGTTAGGGGTTTAG
55618 ATTAATTAGT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
28 18 0.41
29 26 0.59
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.39
Consensus pattern (29 bp):
TTTAAGGTTTAGGGGTTAGGGGTTTAGGA
Found at i:60207 original size:15 final size:15
Alignment explanation
Indices: 60187--60216 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60177 ACTATTTTAA
*
60187 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
60202 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
60217 ATTTATAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:60271 original size:21 final size:21
Alignment explanation
Indices: 60224--60285 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
60214 ATGATTTATA
* *
60224 GTTTAAAGGTTGGGGTTTAAG
1 GTTTAAGGGTTAGGGTTTAAG
60245 GTTTAAGGGTTAGGGTTTAATG
1 GTTTAAGGGTTAGGGTTTAA-G
*
60267 G-TTAAGGGTTTAGGATTTA
1 GTTTAAGGG-TTAGGGTTTA
60286 TGATTTATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 25 0.69
22 11 0.31
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.40
Consensus pattern (21 bp):
GTTTAAGGGTTAGGGTTTAAG
Found at i:60285 original size:7 final size:7
Alignment explanation
Indices: 60275--60313 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
60265 TGGTTAAGGG
*
60275 TTTAGGA
1 TTTATGA
60282 TTTATGA
1 TTTATGA
60289 TTTATGA
1 TTTATGA
60296 TTTATGA
1 TTTATGA
60303 TTTATGA
1 TTTATGA
60310 TTTA
1 TTTA
60314 GGGTTTAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.56
Consensus pattern (7 bp):
TTTATGA
Found at i:60320 original size:21 final size:21
Alignment explanation
Indices: 60271--60320 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
60261 TTAATGGTTA
60271 AGGGTTTAGGATTTATGATTT
1 AGGGTTTAGGATTTATGATTT
* * *
60292 ATGATTTATGATTTATGATTT
1 AGGGTTTAGGATTTATGATTT
60313 AGGGTTTA
1 AGGGTTTA
60321 AGAGATAGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (21 bp):
AGGGTTTAGGATTTATGATTT
Found at i:61898 original size:13 final size:13
Alignment explanation
Indices: 61880--61913 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
61870 ATTTGTGCAT
61880 GACTTTCCTGACA
1 GACTTTCCTGACA
61893 GACTTTCCTGACA
1 GACTTTCCTGACA
*
61906 GACATTCC
1 GACTTTCC
61914 AGAAAGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (13 bp):
GACTTTCCTGACA
Found at i:63069 original size:31 final size:31
Alignment explanation
Indices: 63034--63103 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
63024 CAGCATAACT
63034 TATTGCTGAAGTTATACAGCCACGTTGTTTG
1 TATTGCTGAAGTTATACAGCCACGTTGTTTG
63065 TATTGCTGAAGTTATACAGCCACGTTGTTTG
1 TATTGCTGAAGTTATACAGCCACGTTGTTTG
*
63096 CA-TGCTGA
1 TATTGCTGA
63104 TTACCAGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (31 bp):
TATTGCTGAAGTTATACAGCCACGTTGTTTG
Found at i:63707 original size:41 final size:42
Alignment explanation
Indices: 63647--63762 Score: 139
Period size: 41 Copynumber: 2.8 Consensus size: 42
63637 TTAATTTTTT
* * *
63647 TAAAAGTCATGTTTTTAGCGGCATTTGTGAAA-AAGTGCCGC
1 TAAAAGTTATGTTTTTAGCGGCGTTTGTGAAAGAAGCGCCGC
63688 TAAAAGTTAT-TTTTATAGCGGCGTTTGT-AATAGAAGCGCCGC
1 TAAAAGTTATGTTTT-TAGCGGCGTTTGTGAA-AGAAGCGCCGC
* *
63730 TAAAGGTTATGATTTTTAGCGACGTTTGTGAAA
1 TAAAAGTTATG-TTTTTAGCGGCGTTTGTGAAA
63763 TAAATATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
40 6 0.09
41 22 0.34
42 17 0.27
43 13 0.20
44 6 0.09
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.34
Consensus pattern (42 bp):
TAAAAGTTATGTTTTTAGCGGCGTTTGTGAAAGAAGCGCCGC
Found at i:63878 original size:144 final size:140
Alignment explanation
Indices: 63619--63900 Score: 402
Period size: 143 Copynumber: 2.0 Consensus size: 140
63609 ATTTATGATA
* * *
63619 GAAATAAATATTATTTAATTAATTTTTTTAAAAGTCATGTTTTTAGCGGCATTTGTGAAAAAGTG
1 GAAATAAATATTATTTAATTAATTTTTTTAAAAGTCATGTTGTTAGCAGCATTTGTGAAAAAGCG
* * * *
63684 CCGCTAAAAGTTATTTTTATAGCGGCGTTTGTAATAGAAGCGCCGCTAAAGGTTATGATTTTTAG
66 CCGCTAAAAGTCATTTTTATAGCGGCGTTTGTAATAGAAGCGCCACTAAAGGTCATGATCTTTAG
63749 CGACGTTTGT
131 CGACGTTTGT
*
63759 GAAATAAATATTATTTAATTAAAATATTTTTTAAAAGTCATGTTGTTAGCAGCGTTTGTGAAAAA
1 GAAATAAATATTATTTAATT--AAT-TTTTTTAAAAGTCATGTTGTTAGCAGCATTTGTGAAAAA
* * ** *
63824 GCGCCGTTAAAAGTCATTCTTTATAGTGGCGTTTGTGGTAGAAGCGTCACTAAAGGTCATGATCT
63 GCGCCGCTAAAAGTCATT-TTTATAGCGGCGTTTGTAATAGAAGCGCCACTAAAGGTCATGATCT
*
63889 TTAGCGGCGTTT
127 TTAGCGACGTTT
63901 ATGGTAGAAG
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
140 20 0.16
142 3 0.02
143 51 0.41
144 50 0.40
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (140 bp):
GAAATAAATATTATTTAATTAATTTTTTTAAAAGTCATGTTGTTAGCAGCATTTGTGAAAAAGCG
CCGCTAAAAGTCATTTTTATAGCGGCGTTTGTAATAGAAGCGCCACTAAAGGTCATGATCTTTAG
CGACGTTTGT
Found at i:63883 original size:43 final size:42
Alignment explanation
Indices: 63851--63939 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 42
63841 TCTTTATAGT
*
63851 GGCGTTTGTGGTAGAAGCGTCACTAAAGGTCATGATCTTTAGC
1 GGCGTTTATGGTAGAAGCGTCACTAAAGGTCAT-ATCTTTAGC
**
63894 GGCGTTTATGGTAGAAGCGTCGTTAAAGGTCATGATCTTTAGC
1 GGCGTTTATGGTAGAAGCGTCACTAAAGGTCAT-ATCTTTAGC
63937 GGC
1 GGC
63940 ATTTCTTCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.30
Consensus pattern (42 bp):
GGCGTTTATGGTAGAAGCGTCACTAAAGGTCATATCTTTAGC
Found at i:65849 original size:19 final size:19
Alignment explanation
Indices: 65808--65849 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
65798 ATTGAACTTG
* *
65808 AAAATTGGACCCGAGATCG
1 AAAATTGGACCCGAGAACC
65827 AAAATTGGACCCGAGAACC
1 AAAATTGGACCCGAGAACC
65846 AAAA
1 AAAA
65850 ATCAAAACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AAAATTGGACCCGAGAACC
Found at i:66536 original size:11 final size:12
Alignment explanation
Indices: 66517--66584 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
66507 ATCTAGATAG
66517 TATTT-TATTAA
1 TATTTATATTAA
66528 TA-TTATATTAA
1 TATTTATATTAA
** *
66539 TACGATATATTTA
1 TA-TTTATATTAA
66552 -ATTTA-ATTTAA
1 TATTTATA-TTAA
*
66563 TATTTATATTTA
1 TATTTATATTAA
66575 TATTTATATT
1 TATTTATATT
66585 GATAATATNN
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
10 3 0.07
11 15 0.33
12 19 0.42
13 8 0.18
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (12 bp):
TATTTATATTAA
Found at i:66573 original size:6 final size:6
Alignment explanation
Indices: 66544--66584 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
66534 ATTAATACGA
66544 TATATT TA-ATT TA-ATT TAATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT T-ATATT TATATT TATATT TATATT
66585 GATAATATNN
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 9 0.27
6 20 0.61
7 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:67040 original size:25 final size:25
Alignment explanation
Indices: 67007--67054 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
66997 TTGTAAAGAG
*
67007 AAAATTTTCTAAAGAAATTATTTCA
1 AAAAATTTCTAAAGAAATTATTTCA
* *
67032 AAAAATTTCTAGAGATATTATTT
1 AAAAATTTCTAAAGAAATTATTT
67055 TTATTTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (25 bp):
AAAAATTTCTAAAGAAATTATTTCA
Found at i:68379 original size:18 final size:18
Alignment explanation
Indices: 68339--68382 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
68329 TAATTTTATG
**
68339 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
68357 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
68375 CTTGGGTT
1 ATTGGGTT
68383 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:68977 original size:7 final size:7
Alignment explanation
Indices: 68965--68994 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
68955 CACTTAGGGA
68965 AAAGAAG
1 AAAGAAG
68972 AAAGAAG
1 AAAGAAG
68979 AAAGAAG
1 AAAGAAG
68986 AAAGAAG
1 AAAGAAG
68993 AA
1 AA
68995 CCCCTTTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:75865 original size:14 final size:14
Alignment explanation
Indices: 75848--75893 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
75838 TAAAAAAATG
75848 TTATTAAATTATTA
1 TTATTAAATTATTA
*
75862 TTATTAAATTAGTA
1 TTATTAAATTATTA
75876 TTATTAAATTATTA
1 TTATTAAATTATTA
75890 TTAT
1 TTAT
75894 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:79392 original size:30 final size:30
Alignment explanation
Indices: 79342--79430 Score: 116
Period size: 25 Copynumber: 3.1 Consensus size: 30
79332 ATTTTTTATG
*
79342 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
79373 CCAATATTTGATACTCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
79402 ----TATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
79428 CCA
1 CCA
79431 TAAATATGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
25 22 0.43
26 2 0.04
29 2 0.04
30 18 0.35
31 7 0.14
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:84183 original size:44 final size:43
Alignment explanation
Indices: 84093--84175 Score: 130
Period size: 44 Copynumber: 1.9 Consensus size: 43
84083 AATATTACTA
* *
84093 AATTCACATTTAAAAATAATTATAATTTAATAAAAGTTGAAAT
1 AATTCACATTTAAAAATAATTATAAGTTAAAAAAAGTTGAAAT
*
84136 AATTACACATTTAAAAATAATTATTAGTTAAAAAAAGTTG
1 AATT-CACATTTAAAAATAATTATAAGTTAAAAAAAGTTG
84176 TGATAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 4 0.11
44 32 0.89
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (43 bp):
AATTCACATTTAAAAATAATTATAAGTTAAAAAAAGTTGAAAT
Found at i:85929 original size:26 final size:26
Alignment explanation
Indices: 85900--85985 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
85890 TAGTGATGAA
85900 AGTTCAATGGTTTGAAGTTTGAAGAT
1 AGTTCAATGGTTTGAAGTTTGAAGAT
* * * * * *
85926 AGTTTTGAATTG-ATGTACTTGTTTGATGAA
1 AG--TTCAATGGTTTG-A--AGTTTGAAGAT
85956 AGTTCAATGGTTTGAAGTTTGAAGAT
1 AGTTCAATGGTTTGAAGTTTGAAGAT
85982 AGTT
1 AGTT
85986 TTGAATTGAT
Statistics
Matches: 42, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
26 14 0.33
27 2 0.05
28 14 0.33
29 2 0.05
30 10 0.24
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.42
Consensus pattern (26 bp):
AGTTCAATGGTTTGAAGTTTGAAGAT
Found at i:85979 original size:56 final size:56
Alignment explanation
Indices: 85893--86005 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
85883 TGTGAGTTAG
85893 TGATGAAAGTTCAATGGTTTGAAGTTTGAAGATAGTTTTGAATTGATGTACTTGTT
1 TGATGAAAGTTCAATGGTTTGAAGTTTGAAGATAGTTTTGAATTGATGTACTTGTT
85949 TGATGAAAGTTCAATGGTTTGAAGTTTGAAGATAGTTTTGAATTGATGTACTTGTT
1 TGATGAAAGTTCAATGGTTTGAAGTTTGAAGATAGTTTTGAATTGATGTACTTGTT
86005 T
1 T
86006 CAAAGGTTTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.43
Consensus pattern (56 bp):
TGATGAAAGTTCAATGGTTTGAAGTTTGAAGATAGTTTTGAATTGATGTACTTGTT
Found at i:116354 original size:22 final size:19
Alignment explanation
Indices: 116311--116351 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
116301 GTGAATTTCA
116311 TCTTAGTTTTTTTTTTATT
1 TCTTAGTTTTTTTTTTATT
*
116330 TCTTTGTTTGTTTTATTTATT
1 TCTTAGTTT-TTTT-TTTATT
116351 T
1 T
116352 TCTGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (19 bp):
TCTTAGTTTTTTTTTTATT
Found at i:116860 original size:22 final size:22
Alignment explanation
Indices: 116832--116874 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
116822 ATTTATTCAA
116832 AGCTGTCCATTTGAGTCATAGG
1 AGCTGTCCATTTGAGTCATAGG
* *
116854 AGCTGTCTATTTGAGTTATAG
1 AGCTGTCCATTTGAGTCATAG
116875 CCACTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (22 bp):
AGCTGTCCATTTGAGTCATAGG
Done.