Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold52
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: 1774672
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 127110 characters in sequence are not A, C, G, or T
File 1 of 9
Found at i:147 original size:73 final size:73
Alignment explanation
Indices: 1--144 Score: 218
Period size: 73 Copynumber: 2.0 Consensus size: 73
** * * *
1 TCGGGGTTTGGCGAGGTTTTGATGCTCGGGTTCGGGGTTCGGGGTTCGGGGTTTGGGGTTCGGGG
1 TCGGGGTTTGGCGAGGTTCGGAGGCTCGGGGTCGGGGTTCGGGGTTCGGGGTTTCGGGTTCGGGG
66 TTCGGGGT
66 TTCGGGGT
* *
74 TCGGGGTTTGGCGAGGTTCGGGGGTTCGGGGTCGGGGTTCGGGGTTCGGGG-TTCGGGTTCGGGG
1 TCGGGGTTTGGCGAGGTTCGGAGGCTCGGGGTCGGGGTTCGGGGTTCGGGGTTTCGGGTTCGGGG
138 TTCGGGG
66 TTCGGGG
145 GTTTAGGGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 19 0.30
73 45 0.70
ACGTcount: A:0.02, C:0.13, G:0.55, T:0.30
Consensus pattern (73 bp):
TCGGGGTTTGGCGAGGTTCGGAGGCTCGGGGTCGGGGTTCGGGGTTCGGGGTTTCGGGTTCGGGG
TTCGGGGT
Found at i:199 original size:7 final size:7
Alignment explanation
Indices: 143--1412 Score: 1088
Period size: 7 Copynumber: 177.6 Consensus size: 7
133 CGGGGTTCGG
143 GGGTTTA
1 GGGTTTA
*
150 GGG-TTC
1 GGGTTTA
*
156 GGGTTTC
1 GGGTTTA
*
163 GGG-TTC
1 GGGTTTA
169 GGGTTTCA
1 GGGTTT-A
177 GGGGTTTTAA
1 -GGG-TTT-A
187 GGG-TTA
1 GGGTTTA
*
193 GGGGTTA
1 GGGTTTA
*
200 GGGGGTTA
1 -GGGTTTA
*
208 GGGGTTAA
1 -GGGTTTA
*
216 GGGGTTA
1 GGGTTTA
*
223 GGGGTTA
1 GGGTTTA
230 -GGTTTA
1 GGGTTTA
236 GGGTTTA
1 GGGTTTA
*
243 GGGGGTT-
1 -GGGTTTA
*
250 GGG-GTA
1 GGGTTTA
*
256 GGG-TGA
1 GGGTTTA
262 GGGTTTATA
1 GGG-TT-TA
271 GGG-TTA
1 GGGTTTA
277 GGGTTTAGA
1 GGGTTT--A
*
286 GGGTTAA
1 GGGTTTA
293 GGGTTTA
1 GGGTTTA
*
300 -GGTGTAA
1 GGGT-TTA
307 GGGTTTA
1 GGGTTTA
314 GGGGTTTTA
1 -GGG-TTTA
323 GGGTTTA
1 GGGTTTA
330 GGGTTTA
1 GGGTTTA
337 -GGTTTA
1 GGGTTTA
343 GGGTTTA
1 GGGTTTA
350 GGGTTTA
1 GGGTTTA
357 GGGTTTA
1 GGGTTTA
364 GGG-TTA
1 GGGTTTA
370 GGG-TTA
1 GGGTTTA
376 GGGTTTA
1 GGGTTTA
383 GGGTTTTA
1 GGG-TTTA
391 --GTTTA
1 GGGTTTA
396 GGGTTTTAA
1 GGG-TTT-A
405 GGGTTTA
1 GGGTTTA
412 GGGTTTA
1 GGGTTTA
*
419 GGGGTTA
1 GGGTTTA
426 GGGTTTA
1 GGGTTTA
433 GGGTTTA
1 GGGTTTA
440 GGGTTTAA
1 GGGTTT-A
448 GGG-TTA
1 GGGTTTA
454 -GGTTTAA
1 GGGTTT-A
*
461 GGGGTTGA
1 -GGGTTTA
469 GGGTTTA
1 GGGTTTA
476 GGGTTTA
1 GGGTTTA
483 GGGTTTTA
1 GGG-TTTA
491 GGGGTTTA
1 -GGGTTTA
499 GGGTTTTA
1 GGG-TTTA
507 GGGTTTA
1 GGGTTTA
*
514 GGGGTTA
1 GGGTTTA
521 GGGTTTA
1 GGGTTTA
528 GGGTTTA
1 GGGTTTA
*
535 GGGGTT-
1 GGGTTTA
541 GGGTTTA
1 GGGTTTA
548 GGGTTTA
1 GGGTTTA
555 GGGTTTTATA
1 GGG--TT-TA
565 GGGTTTA
1 GGGTTTA
572 GGGTTTTA
1 GGG-TTTA
580 GGG-TTA
1 GGGTTTA
586 -GGTTTA
1 GGGTTTA
*
592 AGGTTTAA
1 GGGTTT-A
600 GGGTTTA
1 GGGTTTA
607 GGG-TTA
1 GGGTTTA
613 GGGTTTA
1 GGGTTTA
620 GGGTTTCA
1 GGGTTT-A
628 GGGTTTA
1 GGGTTTA
635 GGGTTTA
1 GGGTTTA
*
642 GAGTTTA
1 GGGTTTA
649 GGGTTTAA
1 GGGTTT-A
657 GGGTTTA
1 GGGTTTA
664 GGGTTTTTTA
1 GGG---TTTA
674 GGG-TTA
1 GGGTTTA
680 GGGTTTTA
1 GGG-TTTA
688 GGGTTTA
1 GGGTTTA
695 -GGTTTA
1 GGGTTTA
701 GGGTTTAA
1 GGGTTT-A
709 GGGTTTAA
1 GGGTTT-A
717 GGGTTTA
1 GGGTTTA
724 -GGTTTA
1 GGGTTTA
730 GGGTTTA
1 GGGTTTA
*
737 GGG-TGA
1 GGGTTTA
743 GGG-TTA
1 GGGTTTA
*
749 GTGTTTA
1 GGGTTTA
756 GGGGTTTA
1 -GGGTTTA
764 -GGTGTTA
1 GGGT-TTA
771 GGGTTTA
1 GGGTTTA
778 -GGTTTA
1 GGGTTTA
*
784 GGGTTTTCC
1 GGG-TTT-A
793 GGGTTTTTA
1 GGG--TTTA
802 GGGTTTA
1 GGGTTTA
809 GGGTTTA
1 GGGTTTA
816 -GGTTTA
1 GGGTTTA
**
822 GTTTTTA
1 GGGTTTA
829 GGGTTTA
1 GGGTTTA
836 GGGTTTA
1 GGGTTTA
843 GGGTTT-
1 GGGTTTA
*
849 CGGTTATA
1 GGGTT-TA
*
857 -GGTTGA
1 GGGTTTA
863 GGGTTTA
1 GGGTTTA
*
870 GGGTTTC
1 GGGTTTA
*
877 GGG-TTC
1 GGGTTTA
883 GGGTTTA
1 GGGTTTA
*
890 GGGTGTA
1 GGGTTTA
897 GGGTTTA
1 GGGTTTA
904 GGGTTTA
1 GGGTTTA
*
911 GGGGGTTTTT
1 --GGG-TTTA
*
921 GTTGTTT-
1 G-GGTTTA
*
928 -GTTTTA
1 GGGTTTA
934 GGGTTTTA
1 GGG-TTTA
942 GGG-TTA
1 GGGTTTA
948 GGGTTTA
1 GGGTTTA
955 GGGGTTTA
1 -GGGTTTA
963 GGGTTTA
1 GGGTTTA
970 GGGTTTA
1 GGGTTTA
977 GGGTTTAA
1 GGGTTT-A
985 GGGTTTA
1 GGGTTTA
*
992 GGGTTGGA
1 GGGTT-TA
1000 GGGTTTA
1 GGGTTTA
1007 -GGTTTAA
1 GGGTTT-A
1014 TCGGGTTTA
1 --GGGTTTA
*
1023 GGGTTGA
1 GGGTTTA
1030 GGGTTTA
1 GGGTTTA
1037 GGGTATTA
1 GGGT-TTA
1045 GGG-TTA
1 GGGTTTA
*
1051 GGTTTTTA
1 GG-GTTTA
1059 -GGTTTA
1 GGGTTTA
1065 GGG-TTA
1 GGGTTTA
1071 GGGTTTA
1 GGGTTTA
1078 GGGTTTA
1 GGGTTTA
*
1085 -GG-TTC
1 GGGTTTA
1090 GGGTTTA
1 GGGTTTA
*
1097 AGGTTTA
1 GGGTTTA
*
1104 GGGTTTTCGG
1 GGG-TTT--A
*
1114 GGGTTTC
1 GGGTTTA
1121 GGGTTTA
1 GGGTTTA
*
1128 GTG-TTA
1 GGGTTTA
1134 GGGTTTA
1 GGGTTTA
1141 GGGTTTTA
1 GGG-TTTA
1149 GGGTTTTA
1 GGG-TTTA
1157 GGGTTTA
1 GGGTTTA
1164 GGGTTTA
1 GGGTTTA
1171 GGGTTTA
1 GGGTTTA
1178 GGGTTTGAA
1 GGGTTT--A
1187 GGGTTT-
1 GGGTTTA
*
1193 --TTTATA
1 GGGTT-TA
1199 GGGTTTA
1 GGGTTTA
1206 GGGTTTAA
1 GGGTTT-A
1214 GGGTTTA
1 GGGTTTA
1221 GGGTTTA
1 GGGTTTA
1228 GGG-TTA
1 GGGTTTA
1234 -GGTTTA
1 GGGTTTA
*
1240 GGGGTTA
1 GGGTTTA
1247 GGGTTTTA
1 GGG-TTTA
1255 GGGTTTA
1 GGGTTTA
1262 GGGTTTA
1 GGGTTTA
1269 GGGTGTATTA
1 -GG-GT-TTA
1279 GGGTTTA
1 GGGTTTA
1286 GGGTTTA
1 GGGTTTA
*
1293 GGTTTTA
1 GGGTTTA
1300 GGGTTTA
1 GGGTTTA
*
1307 GGGTGTA
1 GGGTTTA
1314 GGGTTTTA
1 GGG-TTTA
1322 GGGTTTAA
1 GGGTTT-A
*
1330 GGGTTTC
1 GGGTTTA
1337 GGGTTTTA
1 GGG-TTTA
1345 GGGTTTA
1 GGGTTTA
1352 GGGTTTA
1 GGGTTTA
*
1359 GAGTTTA
1 GGGTTTA
*
1366 GAGGTTTC
1 G-GGTTTA
1374 GGGTTTTA
1 GGG-TTTA
*
1382 GGGTTGCA
1 GGGTT-TA
1390 GGGTTTA
1 GGGTTTA
*
1397 -GG-TTC
1 GGGTTTA
1402 GGGTTTA
1 GGGTTTA
1409 GGGT
1 GGGT
1413 GTGCGGGGGT
Statistics
Matches: 1065, Mismatches: 83, Indels: 230
0.77 0.06 0.17
Matches are distributed among these distances:
4 2 0.00
5 19 0.02
6 175 0.16
7 544 0.51
8 233 0.22
9 58 0.05
10 34 0.03
ACGTcount: A:0.15, C:0.01, G:0.42, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:206 original size:8 final size:7
Alignment explanation
Indices: 28--779 Score: 209
Period size: 7 Copynumber: 105.1 Consensus size: 7
18 TTTGATGCTC
*
28 GGGTTCG
1 GGGTTAG
*
35 GGGTTCG
1 GGGTTAG
*
42 GGGTTCG
1 GGGTTAG
*
49 GGGTTTG
1 GGGTTAG
*
56 GGGTTCG
1 GGGTTAG
*
63 GGGTTCG
1 GGGTTAG
*
70 GGGTTCG
1 GGGTTAG
*
77 GGGTTTGG
1 GGG-TTAG
*
85 CGAGGTTCGG
1 -G-GGTT-AG
*
95 GGGTTCG
1 GGGTTAG
*
102 GGG-TCG
1 GGGTTAG
*
108 GGGTTCG
1 GGGTTAG
*
115 GGGTTCG
1 GGGTTAG
*
122 GGGTT-C
1 GGGTTAG
*
128 GGGTTCG
1 GGGTTAG
*
135 GGGTTCGG
1 GGGTT-AG
143 GGGTTTA-
1 GGG-TTAG
*
150 GGGTT-C
1 GGGTTAG
**
156 GGGTTTC
1 GGGTTAG
*
163 GGGTTCG
1 GGGTTAG
*
170 GGTTTCAG
1 GGGTT-AG
*
178 GGGTTTTAA
1 GGG--TTAG
187 GGGTTAG
1 GGGTTAG
194 GGGTTAGG
1 GGGTTA-G
202 GGGTTAG
1 GGGTTAG
209 GGGTTAAG
1 GGGTT-AG
217 GGGTTAG
1 GGGTTAG
224 GGGTTA-
1 GGGTTAG
*
230 GGTTTAG
1 GGGTTAG
*
237 GGTTTAGG
1 GGGTTA-G
245 GGGTT-G
1 GGGTTAG
251 GGG-TA-
1 GGGTTAG
*
256 GGGTGAG
1 GGGTTAG
* *
263 GGTTTATA
1 GGGTTA-G
271 GGGTTAG
1 GGGTTAG
*
278 GGTTTAG
1 GGGTTAG
285 AGGGTTAAG
1 -GGGTT-AG
*
294 GGTTTAG
1 GGGTTAG
* *
301 GTGTAAG
1 GGGTTAG
*
308 GGTTTAG
1 GGGTTAG
315 GGGTTTTAG
1 GGG--TTAG
*
324 GGTTTAG
1 GGGTTAG
*
331 GGTTTA-
1 GGGTTAG
*
337 GGTTTAG
1 GGGTTAG
*
344 GGTTTAG
1 GGGTTAG
*
351 GGTTTAG
1 GGGTTAG
*
358 GGTTTA-
1 GGGTTAG
364 GGGTTA-
1 GGGTTAG
370 GGGTTAG
1 GGGTTAG
*
377 GGTTTAG
1 GGGTTAG
*
384 GGTTTTA-
1 GG-GTTAG
*
391 -GTTTAG
1 GGGTTAG
*
397 GGTTTTAAG
1 GG-GTT-AG
*
406 GGTTTAG
1 GGGTTAG
*
413 GGTTTAG
1 GGGTTAG
420 GGGTTAG
1 GGGTTAG
*
427 GGTTTAG
1 GGGTTAG
*
434 GGTTTAG
1 GGGTTAG
* *
441 GGTTTAA
1 GGGTTAG
448 GGGTTA-
1 GGGTTAG
*
454 GGTTTAAG
1 GGGTT-AG
462 GGGTTGAG
1 GGGTT-AG
*
470 GGTTTAG
1 GGGTTAG
*
477 GGTTTAG
1 GGGTTAG
*
484 GGTTTTAG
1 GG-GTTAG
492 GGGTTTAG
1 GGG-TTAG
*
500 GGTTTTAG
1 GG-GTTAG
*
508 GGTTTAG
1 GGGTTAG
515 GGGTTAG
1 GGGTTAG
*
522 GGTTTAG
1 GGGTTAG
*
529 GGTTTAG
1 GGGTTAG
536 GGGTT-G
1 GGGTTAG
*
542 GGTTTAG
1 GGGTTAG
*
549 GGTTTAG
1 GGGTTAG
*
556 GGTTTTATAG
1 GG--GT-TAG
*
566 GGTTTAG
1 GGGTTAG
*
573 GGTTTTA-
1 GG-GTTAG
580 GGGTTA-
1 GGGTTAG
* *
586 GGTTTAA
1 GGGTTAG
*
593 GGTTTAAG
1 GGGTT-AG
*
601 GGTTTA-
1 GGGTTAG
607 GGGTTAG
1 GGGTTAG
*
614 GGTTTAG
1 GGGTTAG
*
621 GGTTTCAG
1 GGGTT-AG
*
629 GGTTTAG
1 GGGTTAG
*
636 GGTTTAG
1 GGGTTAG
* *
643 AGTTTAG
1 GGGTTAG
*
650 GGTTTAAG
1 GGGTT-AG
*
658 GGTTTAG
1 GGGTTAG
*
665 GGTTTTTTA-
1 GG---GTTAG
674 GGGTTAG
1 GGGTTAG
*
681 GGTTTTAG
1 GG-GTTAG
*
689 GGTTTA-
1 GGGTTAG
*
695 GGTTTAG
1 GGGTTAG
*
702 GGTTTAAG
1 GGGTT-AG
*
710 GGTTTAAG
1 GGGTT-AG
*
718 GGTTTA-
1 GGGTTAG
*
724 GGTTTAG
1 GGGTTAG
*
731 GGTTTA-
1 GGGTTAG
*
737 GGGTGA-
1 GGGTTAG
743 GGGTTAG
1 GGGTTAG
* *
750 TGTTTAG
1 GGGTTAG
757 GGGTTTAG
1 GGG-TTAG
*
765 GTGTTAG
1 GGGTTAG
*
772 GGTTTAG
1 GGGTTAG
779 G
1 G
780 TTTAGGGTTT
Statistics
Matches: 619, Mismatches: 69, Indels: 114
0.77 0.09 0.14
Matches are distributed among these distances:
5 8 0.01
6 92 0.15
7 340 0.55
8 138 0.22
9 26 0.04
10 15 0.02
ACGTcount: A:0.13, C:0.03, G:0.46, T:0.38
Consensus pattern (7 bp):
GGGTTAG
Found at i:274 original size:26 final size:26
Alignment explanation
Indices: 209--280 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
199 AGGGGGTTAG
* * *
209 GGGTTAAG-GGGTTAGGGGTTAGGTTTA
1 GGGTTTAGAGGGTT-GGGG-TAGGGTGA
*
236 GGGTTTAGGGGGTTGGGGTAGGGTGA
1 GGGTTTAGAGGGTTGGGGTAGGGTGA
* *
262 GGGTTTATAGGGTTAGGGT
1 GGGTTTAGAGGGTTGGGGT
281 TTAGAGGGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 22 0.58
27 11 0.29
28 5 0.13
ACGTcount: A:0.15, C:0.00, G:0.53, T:0.32
Consensus pattern (26 bp):
GGGTTTAGAGGGTTGGGGTAGGGTGA
Found at i:1459 original size:22 final size:23
Alignment explanation
Indices: 1419--1498 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 23
1409 GGGTGTGCGG
1419 GGGTTCGGGTTGCCAGGGTTTAC
1 GGGTTCGGGTTGCCAGGGTTTAC
* * *
1442 GGGTTCGGTTTGGC-GGGTTTTC
1 GGGTTCGGGTTGCCAGGGTTTAC
* *
1464 GGTTTCGGG-TGTC--GGTTTAC
1 GGGTTCGGGTTGCCAGGGTTTAC
1484 AGGGTTTCGGGTTGC
1 -GGG-TTCGGGTTGC
1499 GTCGGTTGCG
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 6 0.13
21 5 0.11
22 20 0.44
23 14 0.31
ACGTcount: A:0.05, C:0.15, G:0.44, T:0.36
Consensus pattern (23 bp):
GGGTTCGGGTTGCCAGGGTTTAC
Found at i:1488 original size:29 final size:29
Alignment explanation
Indices: 1435--1585 Score: 78
Period size: 29 Copynumber: 5.4 Consensus size: 29
1425 GGGTTGCCAG
*
1435 GGTTTACGGGTTCGGTTTGGCGGGTTTTC
1 GGTTTACGGGTTCGGTTTGACGGGTTTTC
1464 GGTTT-CGGGTGTCGGTTT-ACAGGG-TTTC
1 GGTTTACGGGT-TCGGTTTGAC-GGGTTTTC
* *
1492 GGGTT--GCG-TCGG-TTG-C-GGTTTTC
1 GGTTTACGGGTTCGGTTTGACGGGTTTTC
*
1515 GGGTTTA-GGGTTTCGGTTT-CCGGGTTTTC
1 -GGTTTACGGG-TTCGGTTTGACGGGTTTTC
*
1544 GGGTTTTCGGGTTTCGGGTTT--CGGG-TTTC
1 -GGTTTACGGG-TTC-GGTTTGACGGGTTTTC
*
1573 GGGTTTAGGGGTT
1 -GGTTTACGGGTT
1586 TAGGGTTTCG
Statistics
Matches: 101, Mismatches: 8, Indels: 27
0.74 0.06 0.20
Matches are distributed among these distances:
22 2 0.02
23 4 0.04
24 7 0.07
25 6 0.06
27 6 0.06
28 19 0.19
29 41 0.41
30 11 0.11
31 5 0.05
ACGTcount: A:0.03, C:0.13, G:0.42, T:0.42
Consensus pattern (29 bp):
GGTTTACGGGTTCGGTTTGACGGGTTTTC
Found at i:1520 original size:30 final size:29
Alignment explanation
Indices: 1476--2277 Score: 136
Period size: 30 Copynumber: 27.7 Consensus size: 29
1466 TTTCGGGTGT
* *
1476 CGGTTTACAGGGTTTCGGGTTGCGTCGGTTG
1 CGGTTTTC-GGGTTTCGGGTT-CGTCGGTTC
*
1507 CGGTTTTCGGGTTTAGGGTT--TCGGTTTC
1 CGGTTTTCGGGTTTCGGGTTCGTCGG-TTC
*
1535 CGGGTTTTCGGGTTTTCGGGTT--TCGGGTTT
1 C-GGTTTTCGGG-TTTCGGGTTCGTC-GGTTC
* * *
1565 CGGGTTTCGGGTTTAGGGGTT--TAGGGTTTC
1 CGGTTTTCGGGTTT-CGGGTTCGT-CGG-TTC
* * *
1595 GGGTTTCCGGG-TTCGGG-T-GTCGGGTTT
1 CGGTTTTCGGGTTTCGGGTTCGTC-GGTTC
* * *
1622 CGGGTTTCGGGTTTAGGAGTTCG--GGTTT
1 CGGTTTTCGGGTTTCGG-GTTCGTCGGTTC
* **
1650 CGGGTTTCGGGTTTCGGGTGGGTTTCGGTTTC
1 CGGTTTTCGGGTTTCGGGTTCG--TCGG-TTC
* * * *
1682 AGG--GTCGGGTTTACCGGTTTCG-GGGTTC
1 CGGTTTTCGGGTTT--CGGGTTCGTCGGTTC
* * *
1710 AGGGTTTCGGGTTTTAGGGTTCG--GGTTTC
1 CGGTTTTCGGG-TTTCGGGTTCGTCGG-TTC
* * ** *
1739 GGGTTTACGGGTTAGGGGTTCG-GGGTT-
1 CGGTTTTCGGGTTTCGGGTTCGTCGGTTC
*
1766 CGGTTTTCGGG-TTCGGGTTTTC-TCGGTTT
1 CGGTTTTCGGGTTTCGGG--TTCGTCGGTTC
*
1795 CGG-TTTAGGGTTTCGGGTT--TC----C
1 CGGTTTTCGGGTTTCGGGTTCGTCGGTTC
*
1817 CGGGTTTTC-GGTTTCGGGTT-ATCCGAGTTTC
1 C-GGTTTTCGGGTTTCGGGTTCGT-CG-G-TTC
*
1848 C-GTGTTTCGGGTTTTCCGGGTTTCG-GGGTTTC
1 CGGT-TTTCGGG-TTT-CGGG-TTCGTCGG-TTC
*
1880 GGGTTTTCGGGTTTCGGGTT--TCGGGTTTC
1 CGGTTTTCGGGTTTCGGGTTCGTC-GG-TTC
* *
1909 GGGGTTTCGGGGTTTC-GG-T-GTCGGGTTTC
1 CGGTTTTC-GGGTTTCGGGTTCGTC-GG-TTC
* *
1938 GGGTTTCCGGGTTTTCGGGTT--TACGGGTTC
1 CGGTTTTCGGG-TTTCGGGTTCGT-C-GGTTC
* * *
1968 CGGGTTTCGGGTTTCGGGGAT-GTCGGGTTT
1 CGGTTTTCGGGTTTC-GGGTTCGTC-GGTTC
*
1998 CGGGTTTCGGGTTTCGGGGTTCG--GGTTGC
1 CGGTTTTCGGGTTTC-GGGTTCGTCGGTT-C
* *
2027 GGGTTTCCGGGATTTCGGGTT--TC---T-
1 CGGTTTTCGGG-TTTCGGGTTCGTCGGTTC
*
2051 -GGATTTCGGGTTTCGGGTT-G-CGGTTC
1 CGGTTTTCGGGTTTCGGGTTCGTCGGTTC
*
2077 GGG-TTTCGGGTTTCGGGTT--TCGGGTTTC
1 CGGTTTTCGGGTTTCGGGTTCGTC-GG-TTC
* * *
2105 GGGTTTACAGGGTTTCGGGTT--TCGGGTTT
1 CGGTTTTC-GGGTTTCGGGTTCGTC-GGTTC
* *
2134 CGGGTTTCGGGTGTTCCCGGGTT--TCGGGTTG
1 CGGTTTTCGGGT-TT--CGGGTTCGTC-GGTTC
* * ** * *
2165 CGGGTTTCAGGGTTTCGGTTTCGGAGTTTT
1 CGGTTTTC-GGGTTTCGGGTTCGTCGGTTC
2195 CGGTTTTGCGGGTTTCGGGTTTCGGTTCGGTT-
1 CGGTTTT-CGGGTTTCGGG-TTC-G-TCGGTTC
* ** *
2227 CGGGTTTCGGGTTTTCGGGTTTTTCGGGTTT
1 CGGTTTTCGGG-TTTCGGGTTCGTCGG-TTC
*
2258 CGGTTTCCGGGTTTCGGGTT
1 CGGTTTTCGGGTTTCGGGTT
2278 TCGGAGTTTC
Statistics
Matches: 600, Mismatches: 85, Indels: 173
0.70 0.10 0.20
Matches are distributed among these distances:
22 11 0.02
23 21 0.04
24 4 0.01
25 2 0.00
26 24 0.04
27 33 0.05
28 87 0.14
29 136 0.23
30 157 0.26
31 71 0.12
32 42 0.07
33 10 0.02
34 2 0.00
ACGTcount: A:0.03, C:0.15, G:0.42, T:0.41
Consensus pattern (29 bp):
CGGTTTTCGGGTTTCGGGTTCGTCGGTTC
Found at i:1528 original size:37 final size:37
Alignment explanation
Indices: 1484--4770 Score: 762
Period size: 37 Copynumber: 87.7 Consensus size: 37
1474 GTCGGTTTAC
*
1484 AGGGTTTCGGGTTGCGTCGG-TTGC-GGTTTTCGGGTTT
1 AGGGTTTCGGGTTCCG--GGTTTGCGGGTTTTCGGGTTT
* *
1521 AGGGTTTCGGTTTCCGGGTTTTCGGGTTTTCGGGTTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * *
1558 CGGGTTTCGGGTTTCGGGTTTAG-GGG-TTTAGGGTTT
1 AGGGTTTCGGGTTCCGGGTTT-GCGGGTTTTCGGGTTT
* *
1594 CGGGTTTCCGGGTT-CGGGTGT-CGGG-TTTCGGGTTT
1 AGGGTTT-CGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* *
1629 CGGGTTTAGGAGTT-CGGGTTT-CGGG-TTTCGGGTTT
1 AGGGTTTCGG-GTTCCGGGTTTGCGGGTTTTCGGGTTT
* *
1664 CGGG--T-GGGTTTC-GGTTT-CAGGG---TCGGGTTT
1 AGGGTTTCGGGTTCCGGGTTTGC-GGGTTTTCGGGTTT
* * *
1694 ACCGGTTTCGGGGTTCAGGGTTT-CGGGTTTTAGGG-TT
1 A-GGGTTTC-GGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
1731 CGGGTTTCGGGTTTACGGGTTAG-GGG--TTCGGGGTT
1 AGGGTTTCGGG-TTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
1766 CGGTTTTCGGGTT-CGGGTTTTCTCGG-TTTC-GGTTT
1 AGGGTTTCGGGTTCCGGGTTTGC-GGGTTTTCGGGTTT
*
1801 AGGGTTTCGGGTTTCCCGGGTTTTC-GG-TTTCGGGTTAT
1 AGGGTTTCGGG-TT-CCGGGTTTGCGGGTTTTCGGGTT-T
* * * * *
1839 CCGAGTTTCCGTGTTTCGGGTTTTCCGGG-TTTCGGGGTTT
1 -AGGGTTT-CGGGTTCCGGG-TTTGCGGGTTTTC-GGGTTT
* *
1879 CGGGTTTTCGGGTTTCGGGTTT-CGGG-TTTCGGGGTTT
1 AGGG-TTTCGGGTTCCGGGTTTGCGGGTTTTC-GGGTTT
* *
1916 CGGGGTTTC-GGTGT-CGGGTTT-CGGGTTTCCGGGTTTT
1 -AGGGTTTCGGGT-TCCGGGTTTGCGGGTTTTCGGG-TTT
* *
1953 CGGGTTTACGGGTTCCGGGTTT-CGGG-TTTCGGGGATGT
1 AGGGTTT-CGGGTTCCGGGTTTGCGGGTTTTC-GGG-TTT
* * * *
1991 CGGGTTTCGGGTTTCGGGTTT-CGGG-GTTCGGGTTG
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
2026 CGGGTTTCCGGGATTTCGGGTTT-CTGGATTTCGGGTTT
1 AGGGTTT-CGGG-TTCCGGGTTTGCGGGTTTTCGGGTTT
* *
2064 CGGGTTGC-GGTT-CGGGTTT-CGGG-TTTCGGGTTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* *
2097 CGGGTTTCGGGTTTACAGGGTTT-CGGG-TTTCGGGTTT
1 AGGGTTTCGGG-TT-CCGGGTTTGCGGGTTTTCGGGTTT
* *
2134 CGGGTTTCGGGTGTTCCCGGGTTT-CGGG-TTGCGGGTTT
1 AGGGTTTC-GG-GTT-CCGGGTTTGCGGGTTTTCGGGTTT
* *
2172 CAGGGTTTC-GGTTTCGGAGTTTTC-GGTTTTGCGGGTTT
1 -AGGGTTTCGGGTTCCGG-GTTTGCGGGTTTT-CGGGTTT
*
2210 CGGGTTTC-GGTT-C-GG-TT-CGGG-TTTCGGGTTTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGG-TTT
* * *
2242 CGGGTTTTTCGGGTTTC-GGTTTCCGGG-TTTCGGGTTT
1 AGGG--TTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * *
2279 CGGAGTTTCCCTGGGTTGCTCGGGTGT-CGGG-TTTCGGGTTC
1 AGG-GTTT--C-GGGTT-C-CGGGTTTGCGGGTTTTCGGGTTT
* * *
2320 CGGGTTTCGGAGTTTC-GGTTT-C-GGTTTTCGGGGTTC
1 AGGGTTTCGG-GTTCCGGGTTTGCGGGTTTTC-GGGTTT
*
2356 CGGGTTTCCGGGTGTCCCGGGTTT-CGGGTTTTCGGGTTT
1 AGGGTTT-CGGGT-T-CCGGGTTTGCGGGTTTTCGGGTTT
* **
2395 CAGGGTTATTCGTGGTTTAC-GGTATTTAGGG-TTTCGGGTATT
1 -AGGG-T-TTCG-GG-TTCCGGGT-TTGCGGGTTTTCGGGT-TT
* * *
2437 CGAGAGTTTTCGGGTTCCGGAGTTT-AGGGTATTCCGGGTTT
1 --AG-GGTTTCGGGTTCCGG-GTTTGCGGGT-TTTCGGGTTT
*
2478 ACGGTTTCGAGGTATTTCCCGGGTTT-CGGG-TTTCGGGTTTTT
1 AGGGTTTCG-GG---TT-CCGGGTTTGCGGGTTTTCGGG--TTT
* *
2520 CGGGTTTTTCGGGGTTGCGAGGTTT-CGGGTTTTTCCCGGAGTTT
1 AGGG--TTTC-GGGTTCCG-GGTTTGCGGG-TTTT--CGG-GTTT
* *
2564 CAGGGTTTCGGGTGTTCGGGTTT-CGGG-TGTCGGGTTT
1 -AGGGTTTCGGGT-TCCGGGTTTGCGGGTTTTCGGGTTT
* *
2601 CCA-GG-TTCGGGTTTCGGATTT-CGGGTTTTCGGGTTT
1 --AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
2637 CGGGTTATCAGGGTTTC-GGTTTTCCGG-TTTCGGGTTT
1 AGGGTT-TC-GGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* *
2674 CGGG-TTCGGAGTTTCCCGGGTTAGGGTTGCGGGTTTCCGGGTTTT
1 AGGGTTTCGG-G-TT-CCGGG-T----TTGCGGGTTTTCGGG-TTT
* *
2719 ACGGGTGTT---GTTTCGGGTATTACGGG-TTTCGGGTTTT
1 A-GGGT-TTCGGGTTCCGGGT-TTGCGGGTTTTCGGG-TTT
* * * *
2756 CGGGGTTTCGGGTTTTCGGGTTT-CGGGTTATCGGGGTT
1 -AGGGTTTCGGG-TTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
2794 CGGTTTTCGGGTATTCGGGTTT-CGGG-TTTCGAGTTT
1 AGGGTTTCGGGT-TCCGGGTTTGCGGGTTTTCGGGTTT
* * *
2830 AGGGTTTTCGGATTGCGGGTTT-CGGAGTTTGGCACGGGTTT
1 AGGG-TTTCGGGTTCCGGGTTTGCGG-GTTT---TCGGGTTT
* * * *
2871 CGGGTGTTCGGGTTTCGGGTTTTCGAGGGGTTTCGGGTTT
1 AGGGT-TTCGGGTTCCGGG-TTT-GCGGGTTTTCGGGTTT
* * * *
2911 CCGCGTTTCGGATTTC-GGTTT-CGGG-TTTCGGGTTTTTTT
1 -AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGG----TTT
* * *
2950 CGGGTCTTCGGGTTTCGGGTTT-CGTG-TTTCGGGTTTT
1 AGGGT-TTCGGGTTCCGGGTTTGCGGGTTTTCGGG-TTT
* * *
2987 CCGGGTTTCGAGTGTTTCGGGTTT-TGGGTTTTCGGGTTT
1 -AGGGTTTCG-G-GTTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
3026 CGGGGTTTCAGGGGTTTCGGGTGT-CGGG--TTCGGGTTG
1 -AGGGTTTC--GGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * *
3063 CGGGTTTCGGGTTATATACGGGTTT-C-GATGTTTCGGGTTT
1 AGGGTTTCGGG---T-TCCGGGTTTGCGGGT-TTTCGGGTTT
* *
3103 TGGGTTATTCGGGTTCAGGGATTT-CGGGTTTTCGGGTTT
1 AGGG-T-TTCGGGTTCCGGG-TTTGCGGGTTTTCGGGTTT
* *
3142 ATCGGTTTCGGGTTTCCGGAGTATT-CGGG-TTTAGGGTTT
1 A-GGGTTTCGGG-TTCCGG-GT-TTGCGGGTTTTCGGGTTT
* ** * *
3181 CGGGTTTC-GGTGGCGGGGTT-CGGGTTTTCGGTTTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
3216 CGGG--TC--TTTACGGG-TTGCGAGGTTAACTCCCGGGTTT
1 AGGGTTTCGGGTTCCGGGTTTGCG-GGTT---T-TCGGGTTT
* *
3253 CCACGGGATTTCGGGTTTCGGGTTT-CAGGGTTTTCGGGTTC
1 --A-GGG-TTTCGGGTTCCGGGTTTGC-GGGTTTTCGGGTTT
* * *
3294 AGGGATTGCGGGTTTTTCGGGTTT-CGGG--TTCGGGTGT
1 AGGG-TTTCGGG--TTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
3331 CGGGTTTCCGGTTTTTCAGGGTTT-CGGG-TTTCGGGTTG
1 AGGGTTT-CGG--GTTCCGGGTTTGCGGGTTTTCGGGTTT
* * *
3369 CGGGTTTCTCGGGTGTCAGGGTTT-CGGGTTTCCGGGTTT
1 AGGG-TT-TCGGGT-TCCGGGTTTGCGGGTTTTCGGGTTT
* * *
3408 CGGGGATTTCGGGTTTCGAGGTTTTCGGGTTTTGCCGGGTCTT
1 -AGGG-TTTCGGGTTCCG-GGTTTGCGGGTTTT--CGGGT-TT
** *
3451 --TTTTTCGGGTTTCGGG-TT-CGGG-TTTCGGGTTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* *
3483 CGGGTTTC--GTTTCGGGTTT-CGGG-TTTCGGGTTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* *
3516 CGGGTTTTTC-GGTATTCGGGTTT-CGGG-TTTCGGGTTTT
1 AGGG--TTTCGGGT-TCCGGGTTTGCGGGTTTTCGGG-TTT
* *
3554 CGGGTTTCGGGTTTTCCTCGGTTT-CGGG-TTTCGGGTTT
1 AGGGTTTCGGG--TTCC-GGGTTTGCGGGTTTTCGGGTTT
* * * *
3592 CCGGGTTTC-GGTTTCGGGTTT-CGGG-TGTC-TGTTT
1 -AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
** * *
3626 CTGGTTTACGGGTTTCGGGTTT-C-GG-TTTCGGGGTT
1 AGGGTTT-CGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
** * *
3661 CCGGTTTCGGGTTTCGGG-TTGCGGG-TTTCTGGTTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * **
3696 CCGGGTTTCGGGTTTACGGGATTGTAAGGG-TTTCGGG-TT
1 -AGGGTTTCGGG-TTCCGGG-TT-TGCGGGTTTTCGGGTTT
*
3735 ACGGG-TTCGGGTTTCCGGGGTT-CGGG-TTTCAGGGTTT
1 A-GGGTTTCGGG-TTCCGGGTTTGCGGGTTTTC-GGGTTT
* * * *
3772 AGGGTTTCGGTTTCCGGGTTTATTCGGAGTATTCTGGTTT
1 AGGGTTTCGGGTTCCGGG-TT-TGCGG-GTTTTCGGGTTT
* *
3812 CACGGGGTTTCGGGTTTCGGG-TT-CGGG--TTCGGGTTG
1 -A--GGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* *
3848 CGGGATTTCGGGTGCCGGG-TT-CGGGTATTTCGGG-TT
1 AGGG-TTTCGGGTTCCGGGTTTGCGGGT-TTTCGGGTTT
* ** * *
3884 ----TTCCGGGTGT-CGGGTTTTAGGGTATTAGGGTTT
1 AGGGTTTCGGGT-TCCGGGTTTGCGGGTTTTCGGGTTT
* * *
3917 CGGGTTATCCGGGTTTCGGGTTT-CTGGTTTTCGGGTTT
1 AGGGTT-T-CGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
3955 CGGGTTTCGGGTTTACGGGTTTTCGGGGTTTCGGG-TT
1 AGGGTTTCGGG-TTCCGGGTTTGCGGGTTTTCGGGTTT
* * *
3992 CGGGTTTTCCGGGTTTCCGACGTTT-CGGGTTATGACGGGTTT
1 AGGG-TTT-CGGG-TTCCG-GGTTTGCGGGTT-T-TCGGGTTT
****** * * *
4034 ATTCACACCGGGTTTTCGGGTTTCCGAGGTTTTCTGGTTT
1 A-GGGTTTCGGG-TTCCGGGTTTGCG-GGTTTTCGGGTTT
* *
4074 CCGGGTTTTCGAGGTTTCGGGTTT--GGGTTTTCGGGTTT
1 -AGGG-TTTCG-GGTTCCGGGTTTGCGGGTTTTCGGGTTT
* *
4112 CGGGATTTCGGGTTTCGGGTTT-CGGG-TTTCGGGTTT
1 AGGG-TTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * *
4148 CGGGATTCGGGTTTCGGAG-TT-CGGG-TTTC-GGTTT
1 AGGGTTTCGGGTTCCGG-GTTTGCGGGTTTTCGGGTTT
* * * * *
4182 CGGGTTTCGGGTTTCGGGTTTTCGGG-GTTCGGATTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
*
4218 ATTCCGAGGTTGACGGGGTT-CGGGTAGTT-CAGGGTTTTCGGGTTT
1 A----G-GGTT-TC-GGGTTCCGGGT--TTGC-GGGTTTTCGGGTTT
* *
4263 CGGGTTTCGGGTTTC-GGTTT-CGGGTATTTACCGGGTTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGT-TTT--CGGGTTT
*
4301 CAGGGTATTCCGGGTTTCCGGGTTT-CAGGGGTTTCGGGATTT
1 -AGGGT-TT-CGGG-TTCCGGGTTTGC-GGGTTTTCGGG-TTT
* *
4343 CGGGTTTCCGGGGTT-CGAGGTTTCCCGGGTTTT--GGTATT
1 AGGGTTT-C-GGGTTCCG-GGTTT-GCGGGTTTTCGGGT-TT
* *
4382 CGGGTTTCGGGTTTCGGGTTT-C-GGTTTT-GGAGTTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGG-GTTT
* * * * * *
4417 -CGGTTTCGGGTTTCGGGTTT-TGGGCTTTAGGGGTT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* *
4452 CGGGATTTCGGGTTTCCGAGGTTTTCGGGTTTTTCGGG-TT
1 AGGG-TTTCGGG-TTCCG-GGTTTGCGGG-TTTTCGGGTTT
* *
4492 CGGGTTTCGGGTTTCGGGTTT-CGGGTTTTCGGG-TT
1 AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
* * * *
4527 ACGGGTTTCGGGTGTTTC-GGTTTCCGGGTACTCCGGGTTT
1 A-GGGTTTC-GG-GTTCCGGGTTTGCGGGT-TTTCGGGTTT
* *
4567 CGGGTTTCGGGTTTTC-GGTTT-CGGG-TTTCGGGTTT
1 AGGGTTTCGGG-TTCCGGGTTTGCGGGTTTTCGGGTTT
* *
4602 CGGGTTTCGGGTTATCGGGTTT-CGGG--TTCGGGTTT
1 AGGGTTTCGGGTT-CCGGGTTTGCGGGTTTTCGGGTTT
* * *
4637 -CGGTTATCGGGTGTTCGGGTTT-C-GG-TTTCGCG---
1 AGGGTT-TCGGGT-TCCGGGTTTGCGGGTTTTCGGGTTT
* *
4669 AGGGTTTGTCGGGTTTCGGCGTTT-CTGGATATTT-GGGTTT
1 AGGG-TT-TCGGGTTCCGG-GTTTGC-GGGT-TTTCGGGTTT
* *
4709 CGGGTTTCGGGTTATCGGGTTT-CGGG-TTTCGGGTTT
1 AGGGTTTCGGGTT-CCGGGTTTGCGGGTTTTCGGGTTT
* * * *
4745 CGGTTTTCGGGTTTCGGGTTTTCGGG
1 AGGGTTTCGGGTTCCGGGTTTGCGGG
4771 GTTCGAGGGT
Statistics
Matches: 2614, Mismatches: 294, Indels: 685
0.73 0.08 0.19
Matches are distributed among these distances:
30 8 0.00
31 28 0.01
32 41 0.02
33 85 0.03
34 152 0.06
35 326 0.12
36 318 0.12
37 419 0.16
38 360 0.14
39 296 0.11
40 208 0.08
41 152 0.06
42 94 0.04
43 62 0.02
44 27 0.01
45 29 0.01
46 7 0.00
48 2 0.00
ACGTcount: A:0.04, C:0.15, G:0.40, T:0.41
Consensus pattern (37 bp):
AGGGTTTCGGGTTCCGGGTTTGCGGGTTTTCGGGTTT
Found at i:2342 original size:6 final size:7
Alignment explanation
Indices: 1279--4804 Score: 2441
Period size: 7 Copynumber: 470.0 Consensus size: 7
1269 GGGTGTATTA
*
1279 GGGTTTA
1 GGGTTTC
*
1286 GGGTTTA
1 GGGTTTC
* *
1293 GGTTTTA
1 GGGTTTC
*
1300 GGGTTTA
1 GGGTTTC
* *
1307 GGGTGTA
1 GGGTTTC
*
1314 GGGTTTTA
1 GGG-TTTC
*
1322 GGGTTTAA
1 GGGTTT-C
1330 GGGTTTC
1 GGGTTTC
*
1337 GGGTTTTA
1 GGG-TTTC
*
1345 GGGTTTA
1 GGGTTTC
*
1352 GGGTTTA
1 GGGTTTC
* *
1359 GAGTTTA
1 GGGTTTC
1366 GAGGTTTC
1 G-GGTTTC
*
1374 GGGTTTTA
1 GGG-TTTC
*
1382 GGGTTGC
1 GGGTTTC
1389 AGGGTTT-
1 -GGGTTTC
*
1396 AGG-TTC
1 GGGTTTC
*
1402 GGGTTTA
1 GGGTTTC
*
1409 GGGTGTGC
1 GGGT-TTC
*
1417 GGGGGTTC
1 -GGGTTTC
*
1425 GGGTTGCC
1 GGGTT-TC
1433 AGGGTTTAC
1 -GGGTTT-C
1442 GGG-TTC
1 GGGTTTC
1448 -GGTTTGGC
1 GGGTTT--C
1456 GGGTTTTC
1 GGG-TTTC
1464 -GGTTTC
1 GGGTTTC
*
1470 GGGTGTC
1 GGGTTTC
1477 -GGTTTAC
1 GGGTTT-C
1484 AGGGTTTC
1 -GGGTTTC
*
1492 GGGTTGC
1 GGGTTTC
*
1499 GTCGGTTGC
1 G--GGTTTC
*
1508 GGTTTTC
1 GGGTTTC
*
1515 GGGTTTA
1 GGGTTTC
1522 GGGTTTC
1 GGGTTTC
1529 -GGTTTCC
1 GGGTTT-C
1536 GGGTTTTC
1 GGG-TTTC
1544 GGGTTTTC
1 GGG-TTTC
1552 GGGTTTC
1 GGGTTTC
1559 GGGTTTC
1 GGGTTTC
1566 GGGTTTC
1 GGGTTTC
*
1573 GGGTTTAG
1 GGGTTT-C
*
1581 GGGTTTA
1 GGGTTTC
1588 GGGTTTC
1 GGGTTTC
1595 GGGTTTCC
1 GGGTTT-C
1603 GGG-TTC
1 GGGTTTC
*
1609 GGGTGTC
1 GGGTTTC
1616 GGGTTTC
1 GGGTTTC
1623 GGGTTTC
1 GGGTTTC
*
1630 GGGTTTA
1 GGGTTTC
1637 GGAG-TTC
1 GG-GTTTC
1644 GGGTTTC
1 GGGTTTC
1651 GGGTTTC
1 GGGTTTC
1658 GGGTTTC
1 GGGTTTC
1665 GGG--T-
1 GGGTTTC
1669 GGGTTTC
1 GGGTTTC
1676 -GGTTTC
1 GGGTTTC
1682 AGGG--TC
1 -GGGTTTC
1688 GGGTTTAC
1 GGGTTT-C
*
1696 CGGTTTC
1 GGGTTTC
*
1703 GGGGTTC
1 GGGTTTC
1710 AGGGTTTC
1 -GGGTTTC
*
1718 GGGTTTTA
1 GGG-TTTC
1726 GGG-TTC
1 GGGTTTC
1732 GGGTTTC
1 GGGTTTC
1739 GGGTTTAC
1 GGGTTT-C
*
1747 GGG-TTA
1 GGGTTTC
*
1753 GGGGTTC
1 GGGTTTC
*
1760 GGGGTTC
1 GGGTTTC
*
1767 GGTTTTC
1 GGGTTTC
1774 GGG-TTC
1 GGGTTTC
1780 GGGTTTTC
1 GGG-TTTC
*
1788 TCGGTTTC
1 -GGGTTTC
*
1796 -GGTTTA
1 GGGTTTC
1802 GGGTTTC
1 GGGTTTC
1809 GGGTTTCCC
1 GGGTTT--C
1818 GGGTTTTC
1 GGG-TTTC
1826 -GGTTTC
1 GGGTTTC
1832 GGGTTATCC
1 GGGTT-T-C
*
1841 GAGTTTCC
1 GGGTTT-C
*
1849 GTGTTTC
1 GGGTTTC
1856 GGGTTTTCC
1 GGG-TTT-C
1865 GGGTTTC
1 GGGTTTC
1872 GGGGTTTC
1 -GGGTTTC
1880 GGGTTTTC
1 GGG-TTTC
1888 GGGTTTC
1 GGGTTTC
1895 GGGTTTC
1 GGGTTTC
1902 GGGTTTC
1 GGGTTTC
1909 GGGGTTTC
1 -GGGTTTC
1917 GGGGTTTC
1 -GGGTTTC
*
1925 -GGTGTC
1 GGGTTTC
1931 GGGTTTC
1 GGGTTTC
1938 GGGTTTCC
1 GGGTTT-C
1946 GGGTTTTC
1 GGG-TTTC
1954 GGGTTTAC
1 GGGTTT-C
*
1962 GGGTTCC
1 GGGTTTC
1969 GGGTTTC
1 GGGTTTC
1976 GGGTTTC
1 GGGTTTC
*
1983 GGGGATGTC
1 -GGG-TTTC
1992 GGGTTTC
1 GGGTTTC
1999 GGGTTTC
1 GGGTTTC
2006 GGGTTTC
1 GGGTTTC
*
2013 GGGGTTC
1 GGGTTTC
*
2020 GGGTTGC
1 GGGTTTC
2027 GGGTTTCC
1 GGGTTT-C
2035 GGGATTTC
1 GGG-TTTC
2043 GGGTTTC
1 GGGTTTC
*
2050 TGGATTTC
1 -GGGTTTC
2058 GGGTTTC
1 GGGTTTC
*
2065 GGGTTGC
1 GGGTTTC
2072 -GG-TTC
1 GGGTTTC
2077 GGGTTTC
1 GGGTTTC
2084 GGGTTTC
1 GGGTTTC
2091 GGGTTTC
1 GGGTTTC
2098 GGGTTTC
1 GGGTTTC
2105 GGGTTTAC
1 GGGTTT-C
2113 AGGGTTTC
1 -GGGTTTC
2121 GGGTTTC
1 GGGTTTC
2128 GGGTTTC
1 GGGTTTC
2135 GGGTTTC
1 GGGTTTC
2142 GGGTGTTCCC
1 GGGT-TT--C
2152 GGGTTTC
1 GGGTTTC
*
2159 GGGTTGC
1 GGGTTTC
2166 GGGTTTC
1 GGGTTTC
2173 AGGGTTTC
1 -GGGTTTC
2181 -GGTTTC
1 GGGTTTC
2187 GGAGTTTTC
1 GG-G-TTTC
*
2196 GGTTTTGC
1 GGGTTT-C
2204 GGGTTTC
1 GGGTTTC
2211 GGGTTTC
1 GGGTTTC
2218 -GG-TTC
1 GGGTTTC
2223 -GG-TTC
1 GGGTTTC
2228 GGGTTTC
1 GGGTTTC
2235 GGGTTTTC
1 GGG-TTTC
2243 GGGTTTTTC
1 GGG--TTTC
2252 GGGTTTC
1 GGGTTTC
2259 -GGTTTCC
1 GGGTTT-C
2266 GGGTTTC
1 GGGTTTC
2273 GGGTTTC
1 GGGTTTC
2280 GGAGTTTCCC
1 GG-GTTT--C
2290 TGGGTTGCTC
1 -GGGTT--TC
*
2300 GGGTGTC
1 GGGTTTC
2307 GGGTTTC
1 GGGTTTC
*
2314 GGGTTCC
1 GGGTTTC
2321 GGGTTTC
1 GGGTTTC
2328 GGAGTTTC
1 GG-GTTTC
2336 -GGTTTC
1 GGGTTTC
*
2342 GGTTTTC
1 GGGTTTC
*
2349 GGGGTTCC
1 -GGGTTTC
2357 GGGTTTCC
1 GGGTTT-C
*
2365 GGGTGTCCC
1 GGGT-T-TC
2374 GGGTTTC
1 GGGTTTC
2381 GGGTTTTC
1 GGG-TTTC
2389 GGGTTTC
1 GGGTTTC
2396 AGGGTTATTC
1 -GGG-T-TTC
2406 GTGGTTTAC
1 G-GGTTT-C
* *
2415 GGTATTTA
1 GG-GTTTC
2423 GGGTTTC
1 GGGTTTC
2430 GGGTATTC
1 GGGT-TTC
2438 GAGAGTTTTC
1 G-G-G-TTTC
*
2448 GGGTTCC
1 GGGTTTC
*
2455 GGAGTTTA
1 GG-GTTTC
2463 GGGTATTCC
1 GGGT-TT-C
2472 GGGTTTAC
1 GGGTTT-C
2480 -GGTTTC
1 GGGTTTC
2486 GAGGTATTTCCC
1 G-GG--TTT--C
2498 GGGTTTC
1 GGGTTTC
2505 GGGTTTC
1 GGGTTTC
2512 GGGTTTTTC
1 GGG--TTTC
2521 GGGTTTTTC
1 GGG--TTTC
*
2530 GGGGTTGC
1 -GGGTTTC
2538 GAGGTTTC
1 G-GGTTTC
2546 GGGTTTTTCCC
1 GGG--TTT--C
2557 GGAGTTTC
1 GG-GTTTC
2565 AGGGTTTC
1 -GGGTTTC
2573 GGGTGTTC
1 GGGT-TTC
2581 GGGTTTC
1 GGGTTTC
*
2588 GGGTGTC
1 GGGTTTC
2595 GGGTTTCC
1 GGGTTT-C
*
2603 AGG-TTC
1 GGGTTTC
2609 GGGTTTC
1 GGGTTTC
*
2616 GGATTTC
1 GGGTTTC
2623 GGGTTTTC
1 GGG-TTTC
2631 GGGTTTC
1 GGGTTTC
2638 GGGTTATC
1 GGGTT-TC
2646 AGGGTTTC
1 -GGGTTTC
*
2654 GGTTTTC
1 GGGTTTC
*
2661 CGGTTTC
1 GGGTTTC
2668 GGGTTTC
1 GGGTTTC
2675 GGG-TTC
1 GGGTTTC
2681 GGAGTTTCCC
1 GG-GTTT--C
*
2691 GGG-TTA
1 GGGTTTC
*
2697 GGGTTGC
1 GGGTTTC
2704 GGGTTTCC
1 GGGTTT-C
2712 GGGTTTTAC
1 GGG-TTT-C
2721 GGGTGTT-
1 GGGT-TTC
2728 --GTTTC
1 GGGTTTC
2733 GGGTATTAC
1 GGGT-TT-C
2742 GGGTTTC
1 GGGTTTC
2749 GGGTTTTC
1 GGG-TTTC
2757 GGGGTTTC
1 -GGGTTTC
2765 GGGTTTTC
1 GGG-TTTC
2773 GGGTTTC
1 GGGTTTC
2780 GGGTTATC
1 GGGTT-TC
*
2788 GGGGTTC
1 GGGTTTC
*
2795 GGTTTTC
1 GGGTTTC
2802 GGGTATTC
1 GGGT-TTC
2810 GGGTTTC
1 GGGTTTC
2817 GGGTTTC
1 GGGTTTC
* *
2824 GAGTTTA
1 GGGTTTC
2831 GGGTTTTC
1 GGG-TTTC
* *
2839 GGATTGC
1 GGGTTTC
2846 GGGTTTC
1 GGGTTTC
2853 GGAGTTTGGCAC
1 GG-GTTT----C
2865 GGGTTTC
1 GGGTTTC
2872 GGGTGTTC
1 GGGT-TTC
2880 GGGTTTC
1 GGGTTTC
2887 GGGTTTTC
1 GGG-TTTC
2895 GAGGGGTTTC
1 ---GGGTTTC
2905 GGGTTTCC
1 GGGTTT-C
*
2913 GCGTTTC
1 GGGTTTC
*
2920 GGATTTC
1 GGGTTTC
2927 -GGTTTC
1 GGGTTTC
2933 GGGTTTC
1 GGGTTTC
2940 GGGTTT-
1 GGGTTTC
*
2946 --TTTTC
1 GGGTTTC
2951 GGGTCTTC
1 GGGT-TTC
2959 GGGTTTC
1 GGGTTTC
2966 GGGTTTC
1 GGGTTTC
*
2973 GTGTTTC
1 GGGTTTC
2980 GGGTTTTCC
1 GGG-TTT-C
2989 GGGTTTC
1 GGGTTTC
2996 GAGTGTTTC
1 G-G-GTTTC
*
3005 GGGTTTT
1 GGGTTTC
3012 GGGTTTTC
1 GGG-TTTC
3020 GGGTTTC
1 GGGTTTC
3027 GGGGTTTC
1 -GGGTTTC
3035 AGGGGTTTC
1 --GGGTTTC
*
3044 GGGTGTC
1 GGGTTTC
3051 GGG-TTC
1 GGGTTTC
*
3057 GGGTTGC
1 GGGTTTC
3064 GGGTTTC
1 GGGTTTC
3071 GGGTTATATAC
1 GGG-T-T-T-C
3082 GGGTTTC
1 GGGTTTC
*
3089 GATGTTTC
1 G-GGTTTC
*
3097 GGGTTTT
1 GGGTTTC
3104 GGGTTATTC
1 GGG-T-TTC
3113 GGG-TTC
1 GGGTTTC
3119 AGGGATTTC
1 -GGG-TTTC
3128 GGGTTTTC
1 GGG-TTTC
3136 GGGTTTATC
1 GGG-TT-TC
3145 -GGTTTC
1 GGGTTTC
3151 GGGTTTCC
1 GGGTTT-C
3159 GGAGTATTC
1 GG-GT-TTC
*
3168 GGGTTTA
1 GGGTTTC
3175 GGGTTTC
1 GGGTTTC
3182 GGGTTTC
1 GGGTTTC
**
3189 -GGTGGC
1 GGGTTTC
*
3195 GGGGTTC
1 GGGTTTC
3202 GGGTTTTC
1 GGG-TTTC
*
3210 GGTTTTC
1 GGGTTTC
3217 GGGTCTTTAC
1 GGG--TTT-C
*
3227 GGGTTGC
1 GGGTTTC
3234 GAGGTTAACTCCC
1 G-GGTT---T--C
3247 GGGTTTCCAC
1 GGGTTT---C
3257 GGGATTTC
1 GGG-TTTC
3265 GGGTTTC
1 GGGTTTC
3272 GGGTTTC
1 GGGTTTC
3279 AGGGTTTTC
1 -GGG-TTTC
3288 GGG-TTC
1 GGGTTTC
*
3294 AGGGATTGC
1 -GGG-TTTC
3303 GGGTTTTTC
1 GGG--TTTC
3312 GGGTTTC
1 GGGTTTC
3319 GGG-TTC
1 GGGTTTC
*
3325 GGGTGTC
1 GGGTTTC
3332 GGGTTTCC
1 GGGTTT-C
*
3340 GGTTTTTC
1 GG-GTTTC
3348 AGGGTTTC
1 -GGGTTTC
3356 GGGTTTC
1 GGGTTTC
*
3363 GGGTTGC
1 GGGTTTC
3370 GGGTTTCTC
1 GGG-TT-TC
*
3379 GGGTGTC
1 GGGTTTC
3386 AGGGTTTC
1 -GGGTTTC
3394 GGGTTTCC
1 GGGTTT-C
3402 GGGTTTC
1 GGGTTTC
3409 GGGGATTTC
1 -GGG-TTTC
3418 GGGTTTC
1 GGGTTTC
3425 GAGGTTTTC
1 G-GG-TTTC
3434 GGGTTTTGCC
1 GGG-TTT--C
3444 GGGTCTT-
1 GGGT-TTC
**
3451 -TTTTTC
1 GGGTTTC
3457 GGGTTTC
1 GGGTTTC
3464 GGG-TTC
1 GGGTTTC
3470 GGGTTTC
1 GGGTTTC
3477 GGGTTTC
1 GGGTTTC
3484 GGGTTTC
1 GGGTTTC
3491 --GTTTC
1 GGGTTTC
3496 GGGTTTC
1 GGGTTTC
3503 GGGTTTC
1 GGGTTTC
3510 GGGTTTC
1 GGGTTTC
3517 GGGTTTTTC
1 GGG--TTTC
3526 -GGTATTC
1 GGGT-TTC
3533 GGGTTTC
1 GGGTTTC
3540 GGGTTTC
1 GGGTTTC
3547 GGGTTTTC
1 GGG-TTTC
3555 GGGTTTC
1 GGGTTTC
3562 GGGTTTTCC
1 GGG-TTT-C
*
3571 TCGGTTTC
1 -GGGTTTC
3579 GGGTTTC
1 GGGTTTC
3586 GGGTTTCC
1 GGGTTT-C
3594 GGGTTTC
1 GGGTTTC
3601 -GGTTTC
1 GGGTTTC
3607 GGGTTTC
1 GGGTTTC
*
3614 GGGTGTC
1 GGGTTTC
*
3621 -TGTTTC
1 GGGTTTC
*
3627 TGGTTTAC
1 GGGTTT-C
3635 GGGTTTC
1 GGGTTTC
3642 GGGTTTC
1 GGGTTTC
3649 -GGTTTC
1 GGGTTTC
*
3655 GGGGTTC
1 GGGTTTC
*
3662 CGGTTTC
1 GGGTTTC
3669 GGGTTTC
1 GGGTTTC
*
3676 GGGTTGC
1 GGGTTTC
3683 GGGTTTC
1 GGGTTTC
*
3690 TGGTTTCC
1 GGGTTT-C
3698 GGGTTTC
1 GGGTTTC
3705 GGGTTTAC
1 GGGTTT-C
*
3713 GGGATTGTAA
1 GGG-TT-T-C
3723 GGGTTTC
1 GGGTTTC
*
3730 GGGTTAC
1 GGGTTTC
3737 GGG-TTC
1 GGGTTTC
3743 GGGTTTCC
1 GGGTTT-C
*
3751 GGGGTTC
1 GGGTTTC
3758 GGGTTTC
1 GGGTTTC
*
3765 AGGGTTTA
1 -GGGTTTC
3773 GGGTTTC
1 GGGTTTC
3780 -GGTTTCC
1 GGGTTT-C
3787 GGGTTTATTC
1 GGG--T-TTC
3797 GGAGTATTC
1 GG-GT-TTC
*
3806 TGGTTTCAC
1 GGGTTT--C
3815 GGGGTTTC
1 -GGGTTTC
3823 GGGTTTC
1 GGGTTTC
3830 GGG-TTC
1 GGGTTTC
3836 GGG-TTC
1 GGGTTTC
*
3842 GGGTTGC
1 GGGTTTC
3849 GGGATTTC
1 GGG-TTTC
**
3857 GGGTGCC
1 GGGTTTC
3864 GGG-TTC
1 GGGTTTC
3870 GGGTATTTC
1 GGG--TTTC
3879 GGGTTTTCC
1 GGG-TTT-C
*
3888 GGGTGTC
1 GGGTTTC
*
3895 GGGTTTTA
1 GGG-TTTC
*
3903 GGGTATTA
1 GGGT-TTC
3911 GGGTTTC
1 GGGTTTC
3918 GGGTTATCC
1 GGGTT-T-C
3927 GGGTTTC
1 GGGTTTC
3934 GGGTTTC
1 GGGTTTC
*
3941 TGGTTTTC
1 -GGGTTTC
3949 GGGTTTC
1 GGGTTTC
3956 GGGTTTC
1 GGGTTTC
3963 GGGTTTAC
1 GGGTTT-C
3971 GGGTTTTC
1 GGG-TTTC
3979 GGGGTTTC
1 -GGGTTTC
3987 GGG-TTC
1 GGGTTTC
3993 GGGTTTTCC
1 GGG-TTT-C
4002 GGGTTTCC
1 GGGTTT-C
*
4010 GACGTTTC
1 G-GGTTTC
4018 GGGTTATGAC
1 GGGTT-T--C
*
4028 GGGTTTAT
1 GGGTTT-C
******
4036 TCACACC
1 GGGTTTC
4043 GGGTTTTC
1 GGG-TTTC
4051 GGGTTTCC
1 GGGTTT-C
4059 GAGGTTTTC
1 G-GG-TTTC
*
4068 TGGTTTCC
1 GGGTTT-C
4076 GGGTTTTC
1 GGG-TTTC
4084 GAGGTTTC
1 G-GGTTTC
4092 GGGTTT-
1 GGGTTTC
4098 GGGTTTTC
1 GGG-TTTC
4106 GGGTTTC
1 GGGTTTC
4113 GGGATTTC
1 GGG-TTTC
4121 GGGTTTC
1 GGGTTTC
4128 GGGTTTC
1 GGGTTTC
4135 GGGTTTC
1 GGGTTTC
4142 GGGTTTC
1 GGGTTTC
*
4149 GGGATTC
1 GGGTTTC
4156 GGGTTTC
1 GGGTTTC
4163 GGAG-TTC
1 GG-GTTTC
4170 GGGTTTC
1 GGGTTTC
4177 -GGTTTC
1 GGGTTTC
4183 GGGTTTC
1 GGGTTTC
4190 GGGTTTC
1 GGGTTTC
4197 GGGTTTTC
1 GGG-TTTC
*
4205 GGGGTTC
1 GGGTTTC
*
4212 GGATTTATTCC
1 GG--GT-TT-C
*
4223 GAGGTTGAC
1 G-GGTT-TC
*
4232 GGGGTTC
1 GGGTTTC
4239 GGGTAGTTC
1 GGGT--TTC
4248 AGGGTTTTC
1 -GGG-TTTC
4257 GGGTTTC
1 GGGTTTC
4264 GGGTTTC
1 GGGTTTC
4271 GGGTTTC
1 GGGTTTC
4278 -GGTTTC
1 GGGTTTC
4284 GGGTATTTACC
1 GGG--TTT--C
4295 GGGTTTC
1 GGGTTTC
4302 AGGGTATTCC
1 -GGGT-TT-C
4312 GGGTTTCC
1 GGGTTT-C
4320 GGGTTTC
1 GGGTTTC
4327 AGGGGTTTC
1 --GGGTTTC
4336 GGGATTTC
1 GGG-TTTC
4344 GGGTTTCC
1 GGGTTT-C
*
4352 GGGGTTC
1 GGGTTTC
4359 GAGGTTTCCC
1 G-GGTTT--C
4369 GGGTTT-
1 GGGTTTC
*
4375 TGGTATTC
1 GGGT-TTC
4383 GGGTTTC
1 GGGTTTC
4390 GGGTTTC
1 GGGTTTC
4397 GGGTTTC
1 GGGTTTC
*
4404 -GGTTTT
1 GGGTTTC
4410 GGAGTTTC
1 GG-GTTTC
4418 -GGTTTC
1 GGGTTTC
4424 GGGTTTC
1 GGGTTTC
*
4431 GGGTTTT
1 GGGTTTC
*
4438 GGGCTTTA
1 GGG-TTTC
*
4446 GGGGTTC
1 GGGTTTC
4453 GGGATTTC
1 GGG-TTTC
4461 GGGTTTCC
1 GGGTTT-C
4469 GAGGTTTTC
1 G-GG-TTTC
4478 GGGTTTTTC
1 GGG--TTTC
4487 GGG-TTC
1 GGGTTTC
4493 GGGTTTC
1 GGGTTTC
4500 GGGTTTC
1 GGGTTTC
4507 GGGTTTC
1 GGGTTTC
4514 GGGTTTTC
1 GGG-TTTC
*
4522 GGGTTAC
1 GGGTTTC
4529 GGGTTTC
1 GGGTTTC
4536 GGGTGTTTC
1 -GG-GTTTC
4545 -GGTTTCC
1 GGGTTT-C
*
4552 GGGTACTCC
1 GGGT--TTC
4561 GGGTTTC
1 GGGTTTC
4568 GGGTTTC
1 GGGTTTC
4575 GGGTTTTC
1 GGG-TTTC
4583 -GGTTTC
1 GGGTTTC
4589 GGGTTTC
1 GGGTTTC
4596 GGGTTTC
1 GGGTTTC
4603 GGGTTTC
1 GGGTTTC
4610 GGGTTATC
1 GGGTT-TC
4618 GGGTTTC
1 GGGTTTC
4625 GGG-TTC
1 GGGTTTC
4631 GGGTTTC
1 GGGTTTC
4638 -GGTTATC
1 GGGTT-TC
4645 GGGTGTTC
1 GGGT-TTC
4653 GGGTTTC
1 GGGTTTC
4660 -GGTTTCGC
1 GGGTTT--C
4668 GAGGGTTTGTC
1 --GGG-TT-TC
4679 GGGTTTC
1 GGGTTTC
4686 GGCGTTTC
1 GG-GTTTC
* *
4694 TGGATATTT
1 -GGGT-TTC
4703 GGGTTTC
1 GGGTTTC
4710 GGGTTTC
1 GGGTTTC
4717 GGGTTATC
1 GGGTT-TC
4725 GGGTTTC
1 GGGTTTC
4732 GGGTTTC
1 GGGTTTC
4739 GGGTTTC
1 GGGTTTC
*
4746 GGTTTTC
1 GGGTTTC
4753 GGGTTTC
1 GGGTTTC
4760 GGGTTTTC
1 GGG-TTTC
*
4768 GGGGTTC
1 GGGTTTC
*
4775 GAGGGTTC
1 G-GGTTTC
*
4783 GCGGTTGC
1 G-GGTTTC
4791 GGGTTTC
1 GGGTTTC
4798 GGGTTTC
1 GGGTTTC
4805 CACCCCAAAC
Statistics
Matches: 2899, Mismatches: 260, Indels: 720
0.75 0.07 0.19
Matches are distributed among these distances:
4 8 0.00
5 27 0.01
6 240 0.08
7 1383 0.48
8 759 0.26
9 331 0.11
10 99 0.03
11 35 0.01
12 14 0.00
13 3 0.00
ACGTcount: A:0.05, C:0.15, G:0.40, T:0.41
Consensus pattern (7 bp):
GGGTTTC
Found at i:2503 original size:26 final size:25
Alignment explanation
Indices: 2306--2520 Score: 78
Period size: 25 Copynumber: 9.0 Consensus size: 25
2296 GCTCGGGTGT
*
2306 CGGGTTTCGGGTTCCGGG--TTT--
1 CGGGTTTCGGGTTTCGGGTATTTCC
2327 CGGAGTTTC-GGTTTC-GGT-TTT-C
1 CGG-GTTTCGGGTTTCGGGTATTTCC
* * *
2349 GGGGTTCCGGGTTTCCGGG--TGTCC
1 CGGGTTTCGGGTTT-CGGGTATTTCC
2373 CGGGTTTCGGGTTTTCGGG--TTT-C
1 CGGGTTTCGGG-TTTCGGGTATTTCC
*
2396 AGGGTTATTCGTGGTTTAC-GGTATTT--
1 CGGG-T-TTCG-GGTTT-CGGGTATTTCC
*
2422 AGGGTTTCGGGTATTCGAGAGT-TTT--
1 CGGGTTTCGGGT-TTCG-G-GTATTTCC
* *
2447 CGGGTTCCGGAGTTTAGGGTA-TT-C
1 CGGGTTTCGG-GTTTCGGGTATTTCC
2471 CGGGTTTAC-GGTTTCGAGGTATTTCC
1 CGGGTTT-CGGGTTTCG-GGTATTTCC
*
2497 CGGGTTTCGGGTTTCGGGTTTTTC
1 CGGGTTTCGGGTTTCGGGTATTTC
2521 GGGTTTTTCG
Statistics
Matches: 154, Mismatches: 14, Indels: 48
0.71 0.06 0.22
Matches are distributed among these distances:
20 2 0.01
21 15 0.10
22 12 0.08
23 20 0.13
24 37 0.24
25 39 0.25
26 26 0.17
27 3 0.02
ACGTcount: A:0.07, C:0.16, G:0.37, T:0.40
Consensus pattern (25 bp):
CGGGTTTCGGGTTTCGGGTATTTCC
Found at i:2520 original size:25 final size:26
Alignment explanation
Indices: 2470--2520 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2460 TTAGGGTATT
2470 CCGGGTTTACGGTTTCGAGGTATTTC
1 CCGGGTTTACGGTTTCGAGGTATTTC
*
2496 CCGGGTTT-CGGGTTTCG-GGTTTTTC
1 CCGGGTTTAC-GGTTTCGAGGTATTTC
2521 GGGTTTTTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.06, C:0.20, G:0.33, T:0.41
Consensus pattern (26 bp):
CCGGGTTTACGGTTTCGAGGTATTTC
Found at i:2535 original size:10 final size:9
Alignment explanation
Indices: 2508--2532 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2498 GGGTTTCGGG
2508 TTTCGGGTT
1 TTTCGGGTT
2517 TTTCGGGTT
1 TTTCGGGTT
2526 TTTCGGG
1 TTTCGGG
2533 GTTGCGAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.36, T:0.52
Consensus pattern (9 bp):
TTTCGGGTT
Found at i:2952 original size:18 final size:19
Alignment explanation
Indices: 2929--2964 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2919 CGGATTTCGG
2929 TTTCGGGT-TTCGGGTTTT
1 TTTCGGGTCTTCGGGTTTT
2947 TTTCGGGTCTTCGGGTTT
1 TTTCGGGTCTTCGGGTTT
2965 CGGGTTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.00, C:0.14, G:0.33, T:0.53
Consensus pattern (19 bp):
TTTCGGGTCTTCGGGTTTT
Found at i:4837 original size:7 final size:7
Alignment explanation
Indices: 4806--4883 Score: 61
Period size: 7 Copynumber: 11.4 Consensus size: 7
4796 TCGGGTTTCC
4806 ACCCCAA
1 ACCCCAA
*
4813 ACCTCAA
1 ACCCCAA
* *
4820 GCACC-A
1 ACCCCAA
4826 ACCCCAA
1 ACCCCAA
4833 ACCCCAA
1 ACCCCAA
* *
4840 ACCTCGA
1 ACCCCAA
4847 ACCCCAA
1 ACCCCAA
*
4854 ACCCAAA
1 ACCCCAA
*
4861 ACCCCTA
1 ACCCCAA
*
4868 A-CCTAA
1 ACCCCAA
*
4874 ACCCCGA
1 ACCCCAA
4881 ACC
1 ACC
4884 TTGACCCCGA
Statistics
Matches: 52, Mismatches: 17, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
6 8 0.15
7 44 0.85
ACGTcount: A:0.40, C:0.51, G:0.04, T:0.05
Consensus pattern (7 bp):
ACCCCAA
Found at i:4851 original size:21 final size:21
Alignment explanation
Indices: 4825--4984 Score: 85
Period size: 21 Copynumber: 7.8 Consensus size: 21
4815 CTCAAGCACC
4825 AACCCCAAACCCCAAACCTCG
1 AACCCCAAACCCCAAACCTCG
* * *
4846 AACCCCAAACCCAAAACCCCT
1 AACCCCAAACCCCAAACCTCG
* * *
4867 AA-CCTAAACCCCGAACCTTG
1 AACCCCAAACCCCAAACCTCG
* **
4887 -ACCCCGAA-CCCTGACCTCG
1 AACCCCAAACCCCAAACCTCG
* * **
4906 AA-CCCGAACCTCAAACCTTT
1 AACCCCAAACCCCAAACCTCG
** * *
4926 AAAACCAAACCCCAAACCCCA
1 AACCCCAAACCCCAAACCTCG
* * * *
4947 AACCCTAAACTCTAAACCTCA
1 AACCCCAAACCCCAAACCTCG
* *
4968 AACCCTAAACCCTAAAC
1 AACCCCAAACCCCAAAC
4985 TCTAAATCTT
Statistics
Matches: 103, Mismatches: 32, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
19 15 0.15
20 25 0.24
21 63 0.61
ACGTcount: A:0.39, C:0.46, G:0.04, T:0.11
Consensus pattern (21 bp):
AACCCCAAACCCCAAACCTCG
Found at i:4890 original size:13 final size:13
Alignment explanation
Indices: 4874--4910 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4864 CCTAACCTAA
*
4874 ACCCCGAACCTTG
1 ACCCCGAACCCTG
4887 ACCCCGAACCCTG
1 ACCCCGAACCCTG
*
4900 ACCTCGAACCC
1 ACCCCGAACCC
4911 GAACCTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.24, C:0.51, G:0.14, T:0.11
Consensus pattern (13 bp):
ACCCCGAACCCTG
Found at i:4940 original size:7 final size:7
Alignment explanation
Indices: 4930--4984 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
4920 ACCTTTAAAA
4930 CCAAACC
1 CCAAACC
4937 CCAAACC
1 CCAAACC
4944 CCAAACC
1 CCAAACC
* *
4951 CTAAACT
1 CCAAACC
*
4958 CTAAACC
1 CCAAACC
*
4965 TCAAACC
1 CCAAACC
*
4972 CTAAACC
1 CCAAACC
*
4979 CTAAAC
1 CCAAAC
4985 TCTAAATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.44, C:0.45, G:0.00, T:0.11
Consensus pattern (7 bp):
CCAAACC
Found at i:4963 original size:28 final size:28
Alignment explanation
Indices: 4932--5014 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 28
4922 CTTTAAAACC
* *
4932 AAACCCCAAACCCCAAACCCTAAACTCT
1 AAACCTCAAACCCTAAACCCTAAACTCT
4960 AAACCTCAAACCCTAAACCCTAAACTCT
1 AAACCTCAAACCCTAAACCCTAAACTCT
* * *
4988 AAATCTTAAACCCTAAATCCTAAACTC
1 AAACCTCAAACCCTAAACCCTAAACTC
5015 GAATTCAAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (28 bp):
AAACCTCAAACCCTAAACCCTAAACTCT
Found at i:4989 original size:7 final size:7
Alignment explanation
Indices: 4946--5014 Score: 54
Period size: 7 Copynumber: 9.9 Consensus size: 7
4936 CCCAAACCCC
*
4946 AAACCCT
1 AAACTCT
4953 AAACTCT
1 AAACTCT
4960 AAAC-CT
1 AAACTCT
*
4966 CAAACCCT
1 -AAACTCT
*
4974 AAACCCT
1 AAACTCT
4981 AAACTCT
1 AAACTCT
4988 AAA-TCTT
1 AAACTC-T
*
4995 AAACCCT
1 AAACTCT
5002 AAA-TCCT
1 AAACT-CT
5009 AAACTC
1 AAACTC
5015 GAATTCAAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
6 4 0.08
7 44 0.85
8 4 0.08
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACTCT
Found at i:4989 original size:14 final size:14
Alignment explanation
Indices: 4932--5012 Score: 83
Period size: 14 Copynumber: 5.8 Consensus size: 14
4922 CTTTAAAACC
* *
4932 AAACCCCAAACCCC
1 AAACCCTAAACCCT
*
4946 AAACCCTAAACTCT
1 AAACCCTAAACCCT
4960 AAA-CCTCAAACCCT
1 AAACCCT-AAACCCT
*
4974 AAACCCTAAACTCT
1 AAACCCTAAACCCT
* *
4988 AAATCTTAAACCCT
1 AAACCCTAAACCCT
*
5002 AAATCCTAAAC
1 AAACCCTAAAC
5013 TCGAATTCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
13 3 0.05
14 50 0.89
15 3 0.05
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACCCTAAACCCT
Found at i:5119 original size:21 final size:21
Alignment explanation
Indices: 5095--5255 Score: 82
Period size: 21 Copynumber: 7.7 Consensus size: 21
5085 GATAATTTAT
5095 CTCTAAATCTTAAACTTTAAA
1 CTCTAAATCTTAAACTTTAAA
* *
5116 CTCTAAATCTT-AGCCTTAAA
1 CTCTAAATCTTAAACTTTAAA
* *
5136 CCCTAAATCTTAACCTTTAAA
1 CTCTAAATCTTAAACTTTAAA
* * * * *
5157 -TCCCAAACCTCAATCTTGAAA
1 CT-CTAAATCTTAAACTTTAAA
* **
5178 CAT-TAAATCGTAAACCCTAAA
1 C-TCTAAATCTTAAACTTTAAA
* **
5199 C-CTTAGGCTTTAAACTTTAAA
1 CTCTAAATC-TTAAACTTTAAA
* *
5220 -TCTTAAATCGTAAACTCTAAA
1 CTC-TAAATCTTAAACTTTAAA
5241 -TCTTAAATCTTAAAC
1 CTC-TAAATCTTAAAC
5256 CTCAAACCTC
Statistics
Matches: 101, Mismatches: 31, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
20 20 0.20
21 77 0.76
22 3 0.03
23 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.33
Consensus pattern (21 bp):
CTCTAAATCTTAAACTTTAAA
Found at i:5136 original size:20 final size:20
Alignment explanation
Indices: 5095--5152 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
5085 GATAATTTAT
*
5095 CTCTAAATCTTAAACTTTAAA
1 CTCTAAATCTT-AACCTTAAA
*
5116 CTCTAAATCTTAGCCTTAAA
1 CTCTAAATCTTAACCTTAAA
*
5136 CCCTAAATCTTAACCTT
1 CTCTAAATCTTAACCTT
5153 TAAATCCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (20 bp):
CTCTAAATCTTAACCTTAAA
Found at i:5165 original size:28 final size:28
Alignment explanation
Indices: 5133--5212 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 28
5123 TCTTAGCCTT
*
5133 AAACCCTAAATCTTAACCTTTAAATCCC
1 AAACCCTAAATCTTAAACTTTAAATCCC
* * **
5161 AAA-CCTCAATCTTGAAACATTAAATCGT
1 AAACCCTAAATCTT-AAACTTTAAATCCC
* **
5189 AAACCCTAAACCTTAGGCTTTAAA
1 AAACCCTAAATCTTAAACTTTAAA
5213 CTTTAAATCT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
27 9 0.22
28 23 0.57
29 8 0.20
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (28 bp):
AAACCCTAAATCTTAAACTTTAAATCCC
Found at i:5225 original size:7 final size:7
Alignment explanation
Indices: 5215--5254 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
5205 GCTTTAAACT
5215 TTAAATC
1 TTAAATC
5222 TTAAATC
1 TTAAATC
*
5229 GTAAA-C
1 TTAAATC
5235 TCTAAATC
1 T-TAAATC
5243 TTAAATC
1 TTAAATC
5250 TTAAA
1 TTAAA
5255 CCTCAAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 1 0.03
7 26 0.90
8 2 0.07
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (7 bp):
TTAAATC
Found at i:12232 original size:15 final size:15
Alignment explanation
Indices: 12212--12241 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12202 GAAATGTTTC
12212 TTTATTTATTTATTT
1 TTTATTTATTTATTT
12227 TTTATTTATTTATTT
1 TTTATTTATTTATTT
12242 ATTTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTATTTATTTATTT
Found at i:12236 original size:19 final size:19
Alignment explanation
Indices: 12212--12248 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
12202 GAAATGTTTC
12212 TTTATTTATTTATTTTTTA
1 TTTATTTATTTATTTTTTA
12231 TTTATTTATTTATTTTTT
1 TTTATTTATTTATTTTTT
12249 TTGCAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTATTTATTTATTTTTTA
Found at i:12250 original size:4 final size:4
Alignment explanation
Indices: 12212--12245 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
12202 GAAATGTTTC
12212 TTTA TTTA TTTA TTT- TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
12246 TTTTTGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:12322 original size:15 final size:15
Alignment explanation
Indices: 12298--12328 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12288 ATAAATGAGG
*
12298 TTGCATAATTTTTTT
1 TTGCAAAATTTTTTT
12313 TTGCAAAATTTTTTT
1 TTGCAAAATTTTTTT
12328 T
1 T
12329 GGTAACATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (15 bp):
TTGCAAAATTTTTTT
Found at i:12408 original size:16 final size:16
Alignment explanation
Indices: 12360--12413 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
12350 GGGCTCGTTA
* *
12360 GGGTTTGGGCTTATTT
1 GGGTTTAGGCTTATTC
* ** *
12376 GGGTTCAGTTTTTTTC
1 GGGTTTAGGCTTATTC
12392 GGGTTTAGGCTTATTC
1 GGGTTTAGGCTTATTC
12408 GGGTTT
1 GGGTTT
12414 GAAATTTTTT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.07, C:0.09, G:0.33, T:0.50
Consensus pattern (16 bp):
GGGTTTAGGCTTATTC
Found at i:12599 original size:19 final size:19
Alignment explanation
Indices: 12555--12600 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
12545 TAATTTTTAA
*
12555 GTAA-ATTTTTATTATATT
1 GTAATATTTTTAATATATT
*
12573 GTTATATTTTTAATATATT
1 GTAATATTTTTAATATATT
12592 -TAATTATTT
1 GTAA-TATTT
12601 ATTTATTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
GTAATATTTTTAATATATT
Found at i:20216 original size:48 final size:47
Alignment explanation
Indices: 20164--20264 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 47
20154 GTTTGGGTTC
* * * *
20164 TCTCAGGTTCAAGTTCTTTGAGGTTCGAGTTTTTTCGAGTTCGAGCTT
1 TCTCAGGTTCAAGTTCTTTCAGGTTCAAGCTTTCTCGAGTTCGAGC-T
*** * *
20212 TCTCAGGTTGGGGTTGTTTCAGGTTCAAGCTTTCTCGGGTTCGAGCT
1 TCTCAGGTTCAAGTTCTTTCAGGTTCAAGCTTTCTCGAGTTCGAGCT
20259 TCTCAG
1 TCTCAG
20265 ATTTGAGTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
47 7 0.16
48 37 0.84
ACGTcount: A:0.13, C:0.19, G:0.28, T:0.41
Consensus pattern (47 bp):
TCTCAGGTTCAAGTTCTTTCAGGTTCAAGCTTTCTCGAGTTCGAGCT
Found at i:22263 original size:16 final size:17
Alignment explanation
Indices: 22242--22274 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22232 TCATGTTTTT
*
22242 ATTTA-TTATTTTCATG
1 ATTTATTTATTGTCATG
22258 ATTTATTTATTGTCATG
1 ATTTATTTATTGTCATG
22275 TGTCCTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (17 bp):
ATTTATTTATTGTCATG
Found at i:22264 original size:20 final size:21
Alignment explanation
Indices: 22228--22268 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
22218 AACTACATAA
*
22228 ATTTTCATGTTTTTATTTATT
1 ATTTTCATGTATTTATTTATT
22249 ATTTTCATG-ATTTATTTATT
1 ATTTTCATGTATTTATTTATT
22269 GTCATGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
ATTTTCATGTATTTATTTATT
Found at i:24214 original size:2 final size:2
Alignment explanation
Indices: 24209--24236 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24199 AATACTGATG
24209 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24237 TTTATTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25820 original size:2 final size:2
Alignment explanation
Indices: 25813--25842 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
25803 GTTATTGTAG
*
25813 GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
25843 TAGCGTAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27434 original size:21 final size:21
Alignment explanation
Indices: 27408--27451 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27398 TTACACATCA
27408 TTTTATGTAAC-AGAGCATTAC
1 TTTTATGTAACTA-AGCATTAC
*
27429 TTTTATGTAGCTAAGCATTAC
1 TTTTATGTAACTAAGCATTAC
27450 TT
1 TT
27452 ACTGGCCCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
TTTTATGTAACTAAGCATTAC
Found at i:30501 original size:2 final size:2
Alignment explanation
Indices: 30494--30522 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30484 TTTATTATGT
30494 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 T
30523 GCAAATGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33942 original size:16 final size:18
Alignment explanation
Indices: 33904--33940 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
33894 AAAATAGTCG
33904 AAAGAGAAAATAAAAGAT
1 AAAGAGAAAATAAAAGAT
33922 AAAGAGAAAA-AAAAGAT
1 AAAGAGAAAATAAAAGAT
33939 AA
1 AA
33941 GATCAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (18 bp):
AAAGAGAAAATAAAAGAT
Found at i:51337 original size:2 final size:2
Alignment explanation
Indices: 51330--51374 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
51320 ATACATAAAA
51330 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51371 AT AT
1 AT AT
51375 TGTAACAAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:53712 original size:38 final size:38
Alignment explanation
Indices: 53670--53769 Score: 155
Period size: 38 Copynumber: 2.6 Consensus size: 38
53660 ACTATTCTTA
* * *
53670 AAAACAAAAACCACTATTCTTAATTAGTTATATGATTC
1 AAAACAAAAACCACTATTCTTAACTAATAATATGATTC
53708 AAAACAAAAACCACTATTCTTAACTAATAATATGATTC
1 AAAACAAAAACCACTATTCTTAACTAATAATATGATTC
* *
53746 AAAACAAAAACCACCATTCGTAAC
1 AAAACAAAAACCACTATTCTTAAC
53770 CGTTGACACA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (38 bp):
AAAACAAAAACCACTATTCTTAACTAATAATATGATTC
Found at i:56217 original size:6 final size:6
Alignment explanation
Indices: 56206--56231 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
56196 GGTTGCTGAA
56206 AAATGC AAATGC AAATGC AAATGC AA
1 AAATGC AAATGC AAATGC AAATGC AA
56232 TTAGTAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AAATGC
Found at i:57035 original size:3 final size:3
Alignment explanation
Indices: 57029--57087 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
57019 TATTTTTGTG
* *
57029 TTA TTA TT- TTA TCA TTA -GA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
57075 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
57088 AGCTATGCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 3 0.06
3 47 0.94
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:58964 original size:2 final size:2
Alignment explanation
Indices: 58959--59000 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
58949 CTCTCTCAAC
58959 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
59001 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:59005 original size:2 final size:2
Alignment explanation
Indices: 59000--59028 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58990 TCTCTCTCTC
59000 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 T
59029 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62586 original size:2 final size:2
Alignment explanation
Indices: 62579--62615 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
62569 TAATTGCAAG
62579 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
62616 ATATGAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:64635 original size:6 final size:6
Alignment explanation
Indices: 64624--64656 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
64614 GTATGAAAAT
*
64624 TTTAAA TTTAAA TTTAGA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
64657 TATGATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:67637 original size:2 final size:2
Alignment explanation
Indices: 67630--67668 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
67620 GAATTATTTT
67630 TA TA TA 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 TA TA TA T
67669 TCATTCTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68473 original size:5 final size:5
Alignment explanation
Indices: 68463--68489 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
68453 CTATAACCAC
68463 GCACA GCACA GCACA GCACA GCACA GC
1 GCACA GCACA GCACA GCACA GCACA GC
68490 GGAGGCACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.41, G:0.22, T:0.00
Consensus pattern (5 bp):
GCACA
Found at i:73400 original size:22 final size:22
Alignment explanation
Indices: 73372--73414 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
73362 TTAGTAACTT
73372 AGTACACTAGCACTCTATACTA
1 AGTACACTAGCACTCTATACTA
*
73394 AGTACACTAGTACTCTATACT
1 AGTACACTAGCACTCTATACT
73415 TTTTAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (22 bp):
AGTACACTAGCACTCTATACTA
Found at i:74386 original size:2 final size:2
Alignment explanation
Indices: 74379--74415 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
74369 ATCTCCTTGG
74379 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
74416 ACACACACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:74420 original size:2 final size:2
Alignment explanation
Indices: 74415--74454 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
74405 CTCTCTCTCT
*
74415 CA CA CA CA CA CA CA CA CA CA CA AA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
74455 AAGGAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:77904 original size:13 final size:13
Alignment explanation
Indices: 77886--77910 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77876 CAAAGATCAG
77886 TGTATCGATACAA
1 TGTATCGATACAA
77899 TGTATCGATACA
1 TGTATCGATACA
77911 TTTTGAGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:77978 original size:19 final size:18
Alignment explanation
Indices: 77954--78051 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
77944 TAGCTTACAT
77954 TGTATCGATACAGAACTTA
1 TGTATCGATACA-AACTTA
77973 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
77986 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
78005 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
78018 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
78038 TGTATCGATACAAA
1 TGTATCGATACAAA
78052 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:77990 original size:32 final size:32
Alignment explanation
Indices: 77949--78049 Score: 177
Period size: 32 Copynumber: 3.1 Consensus size: 32
77939 GGCAGTAGCT
77949 TACATTGTATCGATACAGA-ACTTATGTATCGA
1 TACATTGTATCGATACA-ACACTTATGTATCGA
77981 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
78013 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
78046 TACA
1 TACA
78050 AATCGTTGAA
Statistics
Matches: 67, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
31 1 0.01
32 51 0.76
33 15 0.22
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:77991 original size:13 final size:13
Alignment explanation
Indices: 77973--78029 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
77963 ACAGAACTTA
77973 TGTATCGATACAT
1 TGTATCGATACAT
77986 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
78004 ATGTATCGATACAT
1 -TGTATCGATACAT
78018 TGTATCGATACA
1 TGTATCGATACA
78030 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:82769 original size:2 final size:2
Alignment explanation
Indices: 82762--82813 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
82752 ACCAACAGAT
* * * *
82762 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA CA CA CA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
82805 TA TA TA TA T
1 TA TA TA TA T
82814 TTATGCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:84912 original size:2 final size:2
Alignment explanation
Indices: 84905--84933 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
84895 ATGTAAATGT
84905 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 T
84934 TGAAAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:86452 original size:5 final size:5
Alignment explanation
Indices: 86409--86448 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
86399 TTTGTATCCA
*
86409 TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG CTTGG
1 TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG
86449 CTTGCTATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.03, G:0.40, T:0.57
Consensus pattern (5 bp):
TTTGG
Found at i:86781 original size:3 final size:3
Alignment explanation
Indices: 86773--86813 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
86763 TAATTAACTA
86773 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
86814 GTAAGCGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:88842 original size:2 final size:2
Alignment explanation
Indices: 88835--88862 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
88825 AGACATTTTA
88835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88863 CTCATTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90216 original size:2 final size:2
Alignment explanation
Indices: 90209--90245 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
90199 ATATCTGAAA
*
90209 AT AT AT AT AT GT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90246 TGTTATAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:90232 original size:17 final size:17
Alignment explanation
Indices: 90210--90243 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
90200 TATCTGAAAA
*
90210 TATATATATGTATATAT
1 TATATATATATATATAT
90227 TATATATATATATATAT
1 TATATATATATATATAT
90244 ATTGTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:90233 original size:19 final size:19
Alignment explanation
Indices: 90209--90246 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
90199 ATATCTGAAA
*
90209 ATATATATATGTATATATT
1 ATATATATATATATATATT
90228 ATATATATATATATATATT
1 ATATATATATATATATATT
90247 GTTATAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATATATATATATATATATT
Found at i:90551 original size:13 final size:13
Alignment explanation
Indices: 90533--90557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
90523 TGTTTAGTCT
90533 TGGCAGAAAGAAA
1 TGGCAGAAAGAAA
90546 TGGCAGAAAGAA
1 TGGCAGAAAGAA
90558 TATGTTGGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.32, T:0.08
Consensus pattern (13 bp):
TGGCAGAAAGAAA
Found at i:93895 original size:2 final size:2
Alignment explanation
Indices: 93888--93940 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
93878 GCATTTATAA
93888 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
93930 TC TC TC TC TC T
1 TC TC TC TC TC T
93941 TTGCTTCATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:98511 original size:20 final size:21
Alignment explanation
Indices: 98466--98511 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
98456 ATATCCAAGG
*
98466 CAAACAAAGAAAAATAAAACAT
1 CAAA-AAAGAAAAATAAAAAAT
98488 -AAAAAAGAAAAA-AAAAAAT
1 CAAAAAAGAAAAATAAAAAAT
98507 CAAAA
1 CAAAA
98512 TGCCTCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.27
20 13 0.59
21 3 0.14
ACGTcount: A:0.80, C:0.09, G:0.04, T:0.07
Consensus pattern (21 bp):
CAAAAAAGAAAAATAAAAAAT
Found at i:102918 original size:2 final size:2
Alignment explanation
Indices: 102911--102967 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
102901 TAGTGAGAAT
102911 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
102953 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
102968 TTGATTTGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:103280 original size:2 final size:2
Alignment explanation
Indices: 103273--103302 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
103263 ATCATCAAAG
103273 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
103303 ATATTGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:104581 original size:2 final size:2
Alignment explanation
Indices: 104574--104604 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
104564 AATTATCCAT
104574 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
104605 TTCTGCTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:110911 original size:3 final size:3
Alignment explanation
Indices: 110898--110935 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
110888 ATTAATGTAC
110898 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
110936 CAGGAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:114156 original size:2 final size:2
Alignment explanation
Indices: 114143--114172 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
114133 ATTTGCTATG
*
114143 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
114173 AAAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:131880 original size:2 final size:2
Alignment explanation
Indices: 131844--131868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
131834 CTCAGTAGTG
131844 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
131869 TGTCAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:133368 original size:14 final size:13
Alignment explanation
Indices: 133349--133380 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
133339 GTCTATAAAT
133349 ATAAAATATAAAAA
1 ATAAAAT-TAAAAA
133363 ATAAAATTAAAAA
1 ATAAAATTAAAAA
133376 ATAAA
1 ATAAA
133381 GTCTTTTGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAAAATTAAAAA
Found at i:135322 original size:655 final size:655
Alignment explanation
Indices: 134068--135381 Score: 2610
Period size: 655 Copynumber: 2.0 Consensus size: 655
134058 TCGTAAATAT
*
134068 TGATGCTTATTGCTACCTTACGCAGGGTTTAATGTGGAGACTGTGGAATACAAGAACATTAGCTT
1 TGATACTTATTGCTACCTTACGCAGGGTTTAATGTGGAGACTGTGGAATACAAGAACATTAGCTT
134133 CACTGTTTGGGATGTTGGTGGTCAGGACAAGGTAATACAACAGGAACTCAAAAAATGTTGCAGAA
66 CACTGTTTGGGATGTTGGTGGTCAGGACAAGGTAATACAACAGGAACTCAAAAAATGTTGCAGAA
134198 CTAACCATATATAGTCAGCATTTTACCATAATATTGTTCTTATGGGTCTTCGTGCTTGATGGAAT
131 CTAACCATATATAGTCAGCATTTTACCATAATATTGTTCTTATGGGTCTTCGTGCTTGATGGAAT
134263 AACAATGATTTGCCCTTTTATTCAACTGCACAATCATGTTGCTGTTACAACTGATGAATGTGCTT
196 AACAATGATTTGCCCTTTTATTCAACTGCACAATCATGTTGCTGTTACAACTGATGAATGTGCTT
134328 ATAGACGGTCTTATGCTGATGGCATATTCCATCATCAGCATAGCACGATAATGATAAGCTACATC
261 ATAGACGGTCTTATGCTGATGGCATATTCCATCATCAGCATAGCACGATAATGATAAGCTACATC
134393 TATTAATGCCTCCTTTTCTTTCAAGTTTTTCGTTTGGTGGTTTGAGGAGAGGCTATCCATGTTTT
326 TATTAATGCCTCCTTTTCTTTCAAGTTTTTCGTTTGGTGGTTTGAGGAGAGGCTATCCATGTTTT
134458 GGCTGACACATTATTTGGCATCTTACCTTATTGTGTTTTCCTCGCTATCTAGTGTGCTTATGGAC
391 GGCTGACACATTATTTGGCATCTTACCTTATTGTGTTTTCCTCGCTATCTAGTGTGCTTATGGAC
134523 GTTCCTGTGCTGATTAGATTGTTGTTCATCAACACATAACATATTCATAAGCTACATGTATTGCT
456 GTTCCTGTGCTGATTAGATTGTTGTTCATCAACACATAACATATTCATAAGCTACATGTATTGCT
134588 TCTACCTTGTGTTTCTGTTTTCCTTTTCACTGAATGAGGAAGGCTATTCATTGTGTGGCAAAGAT
521 TCTACCTTGTGTTTCTGTTTTCCTTTTCACTGAATGAGGAAGGCTATTCATTGTGTGGCAAAGAT
134653 GACATGCTTATTTATGTGCATATTTTCCTTGCAGTTATGTTCATTTGTTTGCTCACTGACGGTCT
586 GACATGCTTATTTATGTGCATATTTTCCTTGCAGTTATGTTCATTTGTTTGCTCACTGACGGTCT
134718 TCCTC
651 TCCTC
134723 TGATACTTATTGCTACCTTACGCAGGGTTTAATGTGGAGACTGTGGAATACAAGAACATTAGCTT
1 TGATACTTATTGCTACCTTACGCAGGGTTTAATGTGGAGACTGTGGAATACAAGAACATTAGCTT
134788 CACTGTTTGGGATGTTGGTGGTCAGGACAAGGTAATACAACAGGAACTCAAAAAATGTTGCAGAA
66 CACTGTTTGGGATGTTGGTGGTCAGGACAAGGTAATACAACAGGAACTCAAAAAATGTTGCAGAA
134853 CTAACCATATATAGTCAGCATTTTACCATAATATTGTTCTTATGGGTCTTCGTGCTTGATGGAAT
131 CTAACCATATATAGTCAGCATTTTACCATAATATTGTTCTTATGGGTCTTCGTGCTTGATGGAAT
134918 AACAATGATTTGCCCTTTTATTCAACTGCACAATCATGTTGCTGTTACAACTGATGAATGTGCTT
196 AACAATGATTTGCCCTTTTATTCAACTGCACAATCATGTTGCTGTTACAACTGATGAATGTGCTT
*
134983 ATAGACGGTCTTTTGCTGATGGCATATTCCATCATCAGCATAGCACGATAATGATAAGCTACATC
261 ATAGACGGTCTTATGCTGATGGCATATTCCATCATCAGCATAGCACGATAATGATAAGCTACATC
135048 TATTAATGCCTCCTTTTCTTTCAAGTTTTTCGTTTGGTGGTTTGAGGAGAGGCTATCCATGTTTT
326 TATTAATGCCTCCTTTTCTTTCAAGTTTTTCGTTTGGTGGTTTGAGGAGAGGCTATCCATGTTTT
135113 GGCTGACACATTATTTGGCATCTTACCTTATTGTGTTTTCCTCGCTATCTAGTGTGCTTATGGAC
391 GGCTGACACATTATTTGGCATCTTACCTTATTGTGTTTTCCTCGCTATCTAGTGTGCTTATGGAC
135178 GTTCCTGTGCTGATTAGATTGTTGTTCATCAACACATAACATATTCATAAGCTACATGTATTGCT
456 GTTCCTGTGCTGATTAGATTGTTGTTCATCAACACATAACATATTCATAAGCTACATGTATTGCT
135243 TCTACCTTGTGTTTCTGTTTTCCTTTTCACTGAATGAGGAAGGCTATTCATTGTGTGGCAAAGAT
521 TCTACCTTGTGTTTCTGTTTTCCTTTTCACTGAATGAGGAAGGCTATTCATTGTGTGGCAAAGAT
135308 GACATGCTTATTTATGTGCATATTTTCCTTGCAGTTATGTTCATTTGTTTGCTCACTGACGGTCT
586 GACATGCTTATTTATGTGCATATTTTCCTTGCAGTTATGTTCATTTGTTTGCTCACTGACGGTCT
135373 TCCTC
651 TCCTC
135378 TGAT
1 TGAT
135382 TCGATATTCC
Statistics
Matches: 657, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
655 657 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (655 bp):
TGATACTTATTGCTACCTTACGCAGGGTTTAATGTGGAGACTGTGGAATACAAGAACATTAGCTT
CACTGTTTGGGATGTTGGTGGTCAGGACAAGGTAATACAACAGGAACTCAAAAAATGTTGCAGAA
CTAACCATATATAGTCAGCATTTTACCATAATATTGTTCTTATGGGTCTTCGTGCTTGATGGAAT
AACAATGATTTGCCCTTTTATTCAACTGCACAATCATGTTGCTGTTACAACTGATGAATGTGCTT
ATAGACGGTCTTATGCTGATGGCATATTCCATCATCAGCATAGCACGATAATGATAAGCTACATC
TATTAATGCCTCCTTTTCTTTCAAGTTTTTCGTTTGGTGGTTTGAGGAGAGGCTATCCATGTTTT
GGCTGACACATTATTTGGCATCTTACCTTATTGTGTTTTCCTCGCTATCTAGTGTGCTTATGGAC
GTTCCTGTGCTGATTAGATTGTTGTTCATCAACACATAACATATTCATAAGCTACATGTATTGCT
TCTACCTTGTGTTTCTGTTTTCCTTTTCACTGAATGAGGAAGGCTATTCATTGTGTGGCAAAGAT
GACATGCTTATTTATGTGCATATTTTCCTTGCAGTTATGTTCATTTGTTTGCTCACTGACGGTCT
TCCTC
Found at i:136846 original size:2 final size:2
Alignment explanation
Indices: 136839--136882 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
136829 TTGAATTTGA
* *
136839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
136881 AT
1 AT
136883 TAATGCTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:139629 original size:532 final size:532
Alignment explanation
Indices: 138202--139878 Score: 2550
Period size: 533 Copynumber: 3.2 Consensus size: 532
138192 TACATCTTAC
* * * * *
138202 TTAGTGGTCGAGGTTTTGACAAAATTTATCCAACGATAGCTGAATGTTTTGATCTGGTTCGATTT
1 TTAGTGGTCGAGGTTTCGACAAAGTTTGTCCATCGATAGCTGAATGTTTTGATCTGGTTCGATTC
* * *
138267 ATAGTCGCATCTGTAAATATTTTTTTGTGGTTTTCAAAATACATATTTAATAAAACATGTAATTC
66 ATAGTCGCATCTGCAAACATTTTTTCGTGGTTTTCAAAATACATATTTAATAAAACATGTAATTC
*
138332 ACTCGCTTATATGTTAAAATATTTTTTTTCTTGTTCGATGTGACGTAATATTCTCTCAAAATCTC
131 ACTCGCTTATATGTTAAAAGATTTTTTTTCTTGTTCGATGTGACGTAATATTCTCTCAAAATCTC
* * *
138397 GTAACG-TCTTCGTCATAAGCTTTTTTATCATTTCTATTGACCTCGTCCTCAAAATGTTTAATGT
196 GTAACGTTC-TCGTCACAAGCTTTTCTATCATTTCTATTGACCTCGTCCTTAAAATGTTTAATGT
* *
138461 GTAGCTATGATTGATACATCTTACTTATCTCATCTGTTAGGACATCCAGCATGAAATCAAACAGT
260 GTAGCTATGGTTGATACATCTTACTTATCTCACCTGTTAGG-CATCCAGCATGAAATCAAACAGT
* * *
138526 CAAAAAGTAGTTCTTATACCACGTGTCACGAAATTATTACTTTCCTTCTGAAATACATGCTTGAT
324 CAAAAAGTAGCTCTTATACCACGTGTCACGAGATTATTACTTTCTTTCTGAAATACATGCTTGAT
* ** *
138591 GAAATATGTAATGCATTTACTTATATATTCAAAAAATTTTCTTTTCTCATTTACTGTAAGATTAA
389 GAAATATGTAATGCATTTGCTTATATGCTC-AAAAATTTTCTTTTCTCATTTAATGTAAGATTAA
* *
138656 TGTACTTTATTTTTTTTATAGTGCTTAATGGGATACA--CCAAGTGTTCTTCCTTGCCCTAGGAG
453 TGTACTTTA-TTTTTTTATAGTGCTTAATGGGATACAGTGCAAGTGTTCTTCCTTGCCTTAGGAG
*
138719 GCCTAGCCATCCTTCA
517 GCCTAGCCATCCTTCG
* * * *
138735 TTAGTGGTCGAGGTTTCGACAAAGTTTGTCTATCGAGAGCTGAATGTTTTGATCTGGTTTGATTT
1 TTAGTGGTCGAGGTTTCGACAAAGTTTGTCCATCGATAGCTGAATGTTTTGATCTGGTTCGATTC
138800 ATAGTCGCATCTGCAAACATTTTTTCGTGGTTTTCAAAATACATATTTAATAAAACATGTAATTC
66 ATAGTCGCATCTGCAAACATTTTTTCGTGGTTTTCAAAATACATATTTAATAAAACATGTAATTC
* *
138865 ACTCGCTTATATGTTAAAAGATTTTTTTTCTTGTTCGATGTGATGCAATATTCTCTCAAAATCTC
131 ACTCGCTTATATGTTAAAAGATTTTTTTTCTTGTTCGATGTGACGTAATATTCTCTCAAAATCTC
* * * * * *
138930 GTAACATCCTCGTCACAAGCTTTTCTATCATTTCTATTGACCTCGTCCTTTAAATATTCAATATG
196 GTAACGTTCTCGTCACAAGCTTTTCTATCATTTCTATTGACCTCGTCCTTAAAATGTTTAATGTG
* *
138995 TAGGC-ACGGTTAATACATCTTACTTATCTCACCTGTTAGGGCATCCAGCATGAAATCAAACAGT
261 TA-GCTATGGTTGATACATCTTACTTATCTCACCTGTTA-GGCATCCAGCATGAAATCAAACAGT
* * *
139059 CAAAAAGTAACTCTTATACCACATGTCAC-AGGATTATTACTTTCTTTTTGAAATACATGCTTGA
324 CAAAAAGTAGCTCTTATACCACGTGTCACGA-GATTATTACTTTCTTTCTGAAATACATGCTTGA
* * *
139123 TGAAATATGTAATGTATTCGCTTATATGCTCAAAAATTTTCTTTTCTCATTTAATTTAAGATTAA
388 TGAAATATGTAATGCATTTGCTTATATGCTCAAAAATTTTCTTTTCTCATTTAATGTAAGATTAA
* *
139188 TGTACTTTATTTTTTTAGAGTGCTTAATGGGATACAGTGCAAGTATTCTTCCTTGCCTTAGGAGG
453 TGTACTTTATTTTTTTATAGTGCTTAATGGGATACAGTGCAAGTGTTCTTCCTTGCCTTAGGAGG
*
139253 CCCAGCCATCCTTCG
518 CCTAGCCATCCTTCG
* *
139268 TTAGTGGTCGAGGTTTCAACAAAGTTTGTCCATCGATAGCTGAATGTTTTGATCTGGTTTGATTC
1 TTAGTGGTCGAGGTTTCGACAAAGTTTGTCCATCGATAGCTGAATGTTTTGATCTGGTTCGATTC
* **
139333 ATAGTCGCATCTGCAAACATTTTTTCGTGGTTTTCAAAATACATATTTAATAAAACGTACAATTC
66 ATAGTCGCATCTGCAAACATTTTTTCGTGGTTTTCAAAATACATATTTAATAAAACATGTAATTC
*
139398 ACTCGCTTATATATTAAAAGA-TTTTTTTCTTGTTCGATGTGACGTAATATTCTCTCAAAATCTC
131 ACTCGCTTATATGTTAAAAGATTTTTTTTCTTGTTCGATGTGACGTAATATTCTCTCAAAATCTC
* *
139462 GTAACGTTCTCGTCACAAGCTTTTCTATCATTTCTATTGACCCCATCCTTAAAATGTTTAATGTG
196 GTAACGTTCTCGTCACAAGCTTTTCTATCATTTCTATTGACCTCGTCCTTAAAATGTTTAATGTG
* * *
139527 TAGCTATGGTTGATACATTTTACTTATCTCACCTGTTAGAGCATCCGGTATGAAATCAAACAGTC
261 TAGCTATGGTTGATACATCTTACTTATCTCACCTGTTAG-GCATCCAGCATGAAATCAAACAGTC
* *
139592 AAAAAGTAGCTCTTATACCACGTGTCACGAGATTATTACTTTCTTTCTGAAATGCATGGTTGATG
325 AAAAAGTAGCTCTTATACCACGTGTCACGAGATTATTACTTTCTTTCTGAAATACATGCTTGATG
* * * *
139657 AAATATATATAACGCATTTGCTTATACGCTCAAAAATTTTTCTTTTCTCGTTTAATGTAAGATTA
390 -AA-ATATGTAATGCATTTGCTTATATGCTCAAAAA-TTTTCTTTTCTCATTTAATGTAAGATTA
139722 ATGTAC--T-TTTTTTTATAGTGCTTAATGGGATACAGTGCAAGTGTTC-T--TTGCCTTAGGAG
452 ATGTACTTTATTTTTTTATAGTGCTTAATGGGATACAGTGCAAGTGTTCTTCCTTGCCTTAGGAG
139781 GCCTAGCCATCCTTCG
517 GCCTAGCCATCCTTCG
* * * *
139797 TTAGTGGTCGAGGTTTCGACAAAGTTTGTCCATCGACAACTAAATGTTTTGATCTGATTCGATTC
1 TTAGTGGTCGAGGTTTCGACAAAGTTTGTCCATCGATAGCTGAATGTTTTGATCTGGTTCGATTC
*
139862 ATAGTCACATCTGCAAA
66 ATAGTCGCATCTGCAAA
139879 TGTTTTTCCG
Statistics
Matches: 1042, Mismatches: 90, Indels: 28
0.90 0.08 0.02
Matches are distributed among these distances:
529 102 0.10
531 30 0.03
532 290 0.28
533 556 0.53
534 32 0.03
535 32 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (532 bp):
TTAGTGGTCGAGGTTTCGACAAAGTTTGTCCATCGATAGCTGAATGTTTTGATCTGGTTCGATTC
ATAGTCGCATCTGCAAACATTTTTTCGTGGTTTTCAAAATACATATTTAATAAAACATGTAATTC
ACTCGCTTATATGTTAAAAGATTTTTTTTCTTGTTCGATGTGACGTAATATTCTCTCAAAATCTC
GTAACGTTCTCGTCACAAGCTTTTCTATCATTTCTATTGACCTCGTCCTTAAAATGTTTAATGTG
TAGCTATGGTTGATACATCTTACTTATCTCACCTGTTAGGCATCCAGCATGAAATCAAACAGTCA
AAAAGTAGCTCTTATACCACGTGTCACGAGATTATTACTTTCTTTCTGAAATACATGCTTGATGA
AATATGTAATGCATTTGCTTATATGCTCAAAAATTTTCTTTTCTCATTTAATGTAAGATTAATGT
ACTTTATTTTTTTATAGTGCTTAATGGGATACAGTGCAAGTGTTCTTCCTTGCCTTAGGAGGCCT
AGCCATCCTTCG
Found at i:145467 original size:2 final size:2
Alignment explanation
Indices: 145460--145494 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
145450 ATGAATCATG
*
145460 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
145495 AAGTAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:147370 original size:3 final size:3
Alignment explanation
Indices: 147364--147399 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
147354 TTTTCTTTAT
147364 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
147400 GAACTATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:177401 original size:23 final size:21
Alignment explanation
Indices: 177371--177417 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
177361 CATAGTAACT
177371 TAAAAAATATATTTTTTTTCATC
1 TAAAAAATATA--TTTTTTCATC
*
177394 TAAAAAATGTATTTTTTCATC
1 TAAAAAATATATTTTTTCATC
177415 TAA
1 TAA
177418 TCAATGCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.57
23 10 0.43
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (21 bp):
TAAAAAATATATTTTTTCATC
Found at i:183318 original size:3 final size:3
Alignment explanation
Indices: 183310--183340 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
183300 GCTTAACAGA
*
183310 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
183341 AGAAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:187906 original size:38 final size:36
Alignment explanation
Indices: 187861--187964 Score: 130
Period size: 31 Copynumber: 2.9 Consensus size: 36
187851 TACAGTTTTA
187861 GGGTTTTATATCTTACGTCTCTCAGCATTTAAAGTTTG
1 GGGTTTTATATCTTA--TCTCTCAGCATTTAAAGTTTG
187899 GGG-TTT-TA-C--ATCTCTCAGCATTTAAAGTTTG
1 GGGTTTTATATCTTATCTCTCAGCATTTAAAGTTTG
187930 GGGTTTTATATCTTATATCTCTC-GCATTTAAAGTT
1 GGGTTTTATATC-T-TATCTCTCAGCATTTAAAGTT
187965 AGATACATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 15
0.80 0.00 0.20
Matches are distributed among these distances:
31 24 0.41
32 3 0.05
33 3 0.05
34 1 0.02
35 1 0.02
36 2 0.03
37 15 0.25
38 10 0.17
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.45
Consensus pattern (36 bp):
GGGTTTTATATCTTATCTCTCAGCATTTAAAGTTTG
Found at i:188341 original size:3 final size:3
Alignment explanation
Indices: 188333--188365 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
188323 GTTGCTATGA
188333 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
188366 AATAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:188787 original size:20 final size:20
Alignment explanation
Indices: 188744--188786 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
188734 TCTATGCATC
* *
188744 AAAATAATATTATTTTATTA
1 AAAATAAAATTATTTTATAA
188764 AAAATAAAATTA-TTTATAA
1 AAAATAAAATTATTTTATAA
188783 AAAA
1 AAAA
188787 AATTAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATAAAATTATTTTATAA
Found at i:188908 original size:26 final size:26
Alignment explanation
Indices: 188879--188928 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
188869 TTAATTAATG
*
188879 ATTAATTAAATGATGCTTAACAAATA
1 ATTAAATAAATGATGCTTAACAAATA
*
188905 ATTAAATAAATGATGTTTAACAAA
1 ATTAAATAAATGATGCTTAACAAA
188929 CAAAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (26 bp):
ATTAAATAAATGATGCTTAACAAATA
Found at i:189843 original size:12 final size:12
Alignment explanation
Indices: 189826--189867 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
189816 TGAGTTGAGA
* *
189826 AGAGAGAAAGAG
1 AGAGAGAGAGCG
189838 AGAGAGAGAGCG
1 AGAGAGAGAGCG
*
189850 AGAGCGAGAGCG
1 AGAGAGAGAGCG
189862 AGAGAG
1 AGAGAG
189868 CGAGGGAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.45, C:0.07, G:0.48, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGCG
Found at i:190193 original size:8 final size:9
Alignment explanation
Indices: 190180--190217 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
190170 AATATTTATA
190180 TTTAA-AAT
1 TTTAATAAT
190188 TTTAA-AAT
1 TTTAATAAT
*
190196 TTTAATATT
1 TTTAATAAT
190205 TTTAATAAT
1 TTTAATAAT
190214 TTTA
1 TTTA
190218 TTATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 13 0.48
9 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTAATAAT
Found at i:190226 original size:18 final size:17
Alignment explanation
Indices: 190188--190226 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
190178 TATTTAAAAT
*
190188 TTTAAAATTTTAATATT
1 TTTAAAATTTTAATATA
*
190205 TTTAATAATTTTATTATA
1 TTTAA-AATTTTAATATA
190223 TTTA
1 TTTA
190227 TATTAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAAATTTTAATATA
Found at i:190533 original size:2 final size:2
Alignment explanation
Indices: 190528--190559 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
190518 AAGAGTCGAC
190528 TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
190560 TGTATACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:190960 original size:3 final size:3
Alignment explanation
Indices: 190952--190977 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
190942 AATTCAATTA
190952 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
190978 GGAATTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:191151 original size:3 final size:3
Alignment explanation
Indices: 191143--191174 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
191133 CCTAAAAGCA
191143 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
191175 ACCAAACCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:192289 original size:8 final size:8
Alignment explanation
Indices: 192268--192305 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
192258 TTAAAATAAA
192268 ATAAAA-T
1 ATAAAATT
192275 A-AAAATT
1 ATAAAATT
192282 ATAAAATT
1 ATAAAATT
192290 ATAAAATT
1 ATAAAATT
192298 ATAAAATT
1 ATAAAATT
192306 TTATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 4 0.14
7 3 0.10
8 22 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
ATAAAATT
Found at i:193654 original size:2 final size:2
Alignment explanation
Indices: 193647--193679 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
193637 AATGATCATT
193647 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
193680 TGAATGCATA
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:193898 original size:3 final size:3
Alignment explanation
Indices: 193890--193923 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
193880 TCTAACTCAC
193890 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
193924 GAGCTTCATA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:193997 original size:2 final size:2
Alignment explanation
Indices: 193990--194019 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
193980 ACTATTGAGA
193990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
194020 GATGACATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:196576 original size:25 final size:25
Alignment explanation
Indices: 196511--196586 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 25
196501 TTCAGAAAGC
*
196511 TGCAAGACCATAATAAATCTGTTAA
1 TGCAAGACCATAATAAAGCTGTTAA
**
196536 TGCTCCATATTTCCATAATAAAGCTGTTAA
1 TG---CA-A-GACCATAATAAAGCTGTTAA
196566 TGCAAGACCATAATAAAGCTG
1 TGCAAGACCATAATAAAGCTG
196587 CAAGACCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
25 16 0.39
26 1 0.02
27 2 0.05
28 2 0.05
29 1 0.02
30 19 0.46
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (25 bp):
TGCAAGACCATAATAAAGCTGTTAA
Found at i:210221 original size:36 final size:36
Alignment explanation
Indices: 210174--210246 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
210164 TCCTGTCACA
*
210174 TTGATTTATCTTGCTTCTTGGATACCTTCAAAATGG
1 TTGATTTATCTTCCTTCTTGGATACCTTCAAAATGG
*
210210 TTGATTTATCTTCCTTCTTGGGTACCTTCAAAATGG
1 TTGATTTATCTTCCTTCTTGGATACCTTCAAAATGG
210246 T
1 T
210247 GTTTTCATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (36 bp):
TTGATTTATCTTCCTTCTTGGATACCTTCAAAATGG
Found at i:214002 original size:2 final size:2
Alignment explanation
Indices: 213990--214034 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
213980 AATAAATCAG
213990 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
214033 AT
1 AT
214035 TCTCCTATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:216871 original size:64 final size:64
Alignment explanation
Indices: 216765--216892 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
216755 AAGCAAATGC
* *
216765 TGTTCTCAATCGAATTGATCTTCTCTGTGAGGTATTTGATAATCTTATGATCTTTTAGATTTTT
1 TGTTCTCAATCGAATTGATCTTCTCTGTGAGGTATTTGATAATCTTAGGATCTTTTACATTTTT
* *
216829 TGTTTTCAATCGAATTGATCTTCTCTGTGAGGTATTTGATAATCTTAGGATTTTTTACATTTTT
1 TGTTCTCAATCGAATTGATCTTCTCTGTGAGGTATTTGATAATCTTAGGATCTTTTACATTTTT
216893 GGAACATTGG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.51
Consensus pattern (64 bp):
TGTTCTCAATCGAATTGATCTTCTCTGTGAGGTATTTGATAATCTTAGGATCTTTTACATTTTT
Found at i:223417 original size:2 final size:2
Alignment explanation
Indices: 223410--223445 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
223400 TTCCATTTTC
223410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
223446 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 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):
AT
Found at i:229547 original size:2 final size:2
Alignment explanation
Indices: 229542--229577 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
229532 TCCCCCCCCC
229542 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
229578 TTTTGGTACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:237033 original size:2 final size:2
Alignment explanation
Indices: 237026--237061 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
237016 TGGGGTGGCA
237026 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
237062 GTGTAGGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:237537 original size:38 final size:36
Alignment explanation
Indices: 237462--237536 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 36
237452 TTAGCAGGTA
*
237462 TTAATTTA-TATTATTTAAATATTTTTTTAAATTTT
1 TTAATTTATTATTATTTAAATATCTTTTTAAATTTT
237497 TTAATTTATTATTAATTTTAAAT-TACTTTTTAATATTTT
1 TTAATTTATTATT-A-TTTAAATAT-CTTTTTAA-ATTTT
237536 T
1 T
237537 ATTTTTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
35 8 0.24
36 4 0.12
37 2 0.06
38 14 0.41
39 6 0.18
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (36 bp):
TTAATTTATTATTATTTAAATATCTTTTTAAATTTT
Found at i:238150 original size:16 final size:16
Alignment explanation
Indices: 238131--238166 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
238121 ATATATTTTA
*
238131 ATATAAATTATTAAAT
1 ATATAAAATATTAAAT
*
238147 ATATAAAATCTTAAAT
1 ATATAAAATATTAAAT
238163 ATAT
1 ATAT
238167 TTATATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATATTAAAT
Found at i:238583 original size:2 final size:2
Alignment explanation
Indices: 238576--238617 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
238566 CACCCAACAT
238576 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
238618 GGGGCTTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:242911 original size:15 final size:15
Alignment explanation
Indices: 242891--242919 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
242881 TGTAACTTAA
242891 GATTCTCCGAGTTTT
1 GATTCTCCGAGTTTT
242906 GATTCTCCGAGTTT
1 GATTCTCCGAGTTT
242920 GACAGGTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (15 bp):
GATTCTCCGAGTTTT
Found at i:243200 original size:56 final size:56
Alignment explanation
Indices: 243102--243215 Score: 131
Period size: 56 Copynumber: 2.0 Consensus size: 56
243092 GTTTTGGTCC
* * * * ** * *
243102 TGATGACTTTCCTGACTTCTTGTTTCCATGTTACTTTGAAAGT-TCCAATTAAGGAG
1 TGATGACTTTACTGACTACCTGTTTCCAGGCCACTCTCAAAGTAT-CAATTAAGGAG
*
243158 TGATGACTTTACTGACTACCTGTTTCCAGGCCACTCTCAAAGTATCAATTGAGGAG
1 TGATGACTTTACTGACTACCTGTTTCCAGGCCACTCTCAAAGTATCAATTAAGGAG
243214 TG
1 TG
243216 TTTCTGGGAG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
56 47 0.98
57 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (56 bp):
TGATGACTTTACTGACTACCTGTTTCCAGGCCACTCTCAAAGTATCAATTAAGGAG
Found at i:255253 original size:6 final size:5
Alignment explanation
Indices: 255244--255309 Score: 51
Period size: 6 Copynumber: 11.6 Consensus size: 5
255234 CAAGGAGAAC
*
255244 TTTAGT TTTAT TTTAT TTTATT TATTAA TTTAT TATTAT TATTAT TATTAT
1 TTTA-T TTTAT TTTAT TTTA-T T-TTAT TTTAT T-TTAT T-TTAT T-TTAT
255295 TATTAT TATTAT TTT
1 T-TTAT T-TTAT TTT
255310 TGAGTTTTGA
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
5 16 0.29
6 36 0.65
7 3 0.05
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (5 bp):
TTTAT
Found at i:255281 original size:3 final size:3
Alignment explanation
Indices: 255251--255307 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
255241 AACTTTAGTT
*
255251 TTA TT- TTA TT- TTA TTTA TTA AT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
255294 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
255308 TTTGAGTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:263815 original size:2 final size:2
Alignment explanation
Indices: 263808--263839 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
263798 TTATTGAGAC
263808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
263840 GTATGAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:264112 original size:12 final size:12
Alignment explanation
Indices: 264095--264119 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
264085 TTATAACAAG
264095 GCTACTCAAGCA
1 GCTACTCAAGCA
264107 GCTACTCAAGCA
1 GCTACTCAAGCA
264119 G
1 G
264120 AAGACGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.16
Consensus pattern (12 bp):
GCTACTCAAGCA
Found at i:273915 original size:3 final size:3
Alignment explanation
Indices: 273907--273938 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
273897 CCAACTCAGT
273907 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
273939 GTACCCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:274350 original size:19 final size:19
Alignment explanation
Indices: 274326--274362 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
274316 ATATATATAT
274326 ATATATATATTTTAAAAAA
1 ATATATATATTTTAAAAAA
*
274345 ATATATTTATTTTAAAAA
1 ATATATATATTTTAAAAA
274363 TAATTTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATATATATTTTAAAAAA
Found at i:285354 original size:30 final size:29
Alignment explanation
Indices: 285302--285390 Score: 98
Period size: 30 Copynumber: 3.2 Consensus size: 29
285292 ACAACCGAAT
* *
285302 AGAAAAGTATAAATTGGATTAAAAAGAAA
1 AGAAAAGTATAAACTAGATTAAAAAGAAA
285331 AGAAAAGTATAACACTAGATTAAAAAGAAA
1 AGAAAAGTATAA-ACTAGATTAAAAAGAAA
*
285361 AG--TA-TA-AAACTAGATTAAAAA-AAA
1 AGAAAAGTATAAACTAGATTAAAAAGAAA
*
285385 AAAAAA
1 AGAAAA
285391 CAAACTTTGT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
24 4 0.08
25 13 0.25
26 3 0.06
27 2 0.04
28 1 0.02
29 12 0.23
30 17 0.33
ACGTcount: A:0.66, C:0.03, G:0.12, T:0.18
Consensus pattern (29 bp):
AGAAAAGTATAAACTAGATTAAAAAGAAA
Found at i:285361 original size:25 final size:25
Alignment explanation
Indices: 285328--285386 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
285318 GATTAAAAAG
*
285328 AAAAGAAAAGTATAACACTAGATTA
1 AAAAGAAAAGTATAAAACTAGATTA
285353 AAAAGAAAAGTATAAAACTAGATTA
1 AAAAGAAAAGTATAAAACTAGATTA
*
285378 AAAAAAAAA
1 AAAAGAAAA
285387 AAAACAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (25 bp):
AAAAGAAAAGTATAAAACTAGATTA
Found at i:285395 original size:25 final size:25
Alignment explanation
Indices: 285318--285396 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 25
285308 GTATAAATTG
285318 GATTAAAAAGAAAAGAAAAGTATAACACTA
1 GATTAAAAAGAAAA-AAAA--A-AA-ACTA
** *
285348 GATTAAAAAGAAAAGTATAAAACTA
1 GATTAAAAAGAAAAAAAAAAAACTA
285373 GATTAAAAA-AAAAAAAAACAAACT
1 GATTAAAAAGAAAAAAAAA-AAACT
285397 TTGTCGTGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
24 6 0.14
25 18 0.43
26 2 0.05
27 1 0.02
29 1 0.02
30 14 0.33
ACGTcount: A:0.67, C:0.06, G:0.10, T:0.16
Consensus pattern (25 bp):
GATTAAAAAGAAAAAAAAAAAACTA
Found at i:291076 original size:2 final size:2
Alignment explanation
Indices: 291069--291105 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
291059 TTAGCAGCAA
291069 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
291106 ATTTGGAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:291636 original size:3 final size:3
Alignment explanation
Indices: 291628--291653 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
291618 TATATAAAGC
291628 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
291654 TTCAAGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:292057 original size:13 final size:13
Alignment explanation
Indices: 292039--292069 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
292029 GGATTACTCG
292039 TTTTTATTTTTAT
1 TTTTTATTTTTAT
292052 TTTTTATTTTTAT
1 TTTTTATTTTTAT
292065 TTTTT
1 TTTTT
292070 TGCTCTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:292069 original size:7 final size:6
Alignment explanation
Indices: 292039--292068 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
292029 GGATTACTCG
292039 TTTTTA TTTTTA TTTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA -TTTTTA TTTTTA TTTTT
292069 TTGCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:295693 original size:27 final size:27
Alignment explanation
Indices: 295655--295707 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
295645 CTGCCAGAAG
* *
295655 GCATATCTATATGAAGATGTCAATGTA
1 GCATATCTATATAAAGATGCCAATGTA
*
295682 GCATATGTATATAAAGATGCCAATGT
1 GCATATCTATATAAAGATGCCAATGT
295708 TCTGTAAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (27 bp):
GCATATCTATATAAAGATGCCAATGTA
Done.