Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 1 of 175
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--1075 Score: 1049
Period size: 7 Copynumber: 152.7 Consensus size: 7
1 TAAACCC
1 TAAACCC
8 TAAACCC
1 TAAACCC
15 TAAACCC
1 TAAACCC
22 TAAACCC
1 TAAACCC
29 TAAACCC
1 TAAACCC
36 TAAACCC
1 TAAACCC
43 TAAACCC
1 TAAACCC
50 TAAACCC
1 TAAACCC
57 TAAACCC
1 TAAACCC
64 TAAACCC
1 TAAACCC
71 TAAACCC
1 TAAACCC
78 TAAACCC
1 TAAACCC
85 TAAACCC
1 TAAACCC
92 TAAACCC
1 TAAACCC
99 TAAACCC
1 TAAACCC
106 TAAACCC
1 TAAACCC
113 TAAACCC
1 TAAACCC
120 TAAACCC
1 TAAACCC
127 TAAACCC
1 TAAACCC
134 TAAACCC
1 TAAACCC
141 TAAACCC
1 TAAACCC
148 TAAACCC
1 TAAACCC
155 TAAACCC
1 TAAACCC
162 TAAACCC
1 TAAACCC
169 TAAAACCC
1 T-AAACCC
*
177 TGAACCC
1 TAAACCC
184 TAAA-CC
1 TAAACCC
*
190 TGAACCC
1 TAAACCC
*
197 TGAACCC
1 TAAACCC
*
204 TGAACCC
1 TAAACCC
*
211 TGAACCC
1 TAAACCC
*
218 TGAACCC
1 TAAACCC
*
225 TGAACCC
1 TAAACCC
*
232 TGAACCC
1 TAAACCC
*
239 TGAACCC
1 TAAACCC
*
246 TGAACCC
1 TAAACCC
*
253 TGAACCC
1 TAAACCC
*
260 TGAACCC
1 TAAACCC
*
267 TGAACCC
1 TAAACCC
*
274 TGAACCC
1 TAAACCC
*
281 TGAACCC
1 TAAACCC
*
288 TGAACCC
1 TAAACCC
*
295 TGAACCC
1 TAAACCC
*
302 TGAACCC
1 TAAACCC
*
309 TGAACCC
1 TAAACCC
*
316 TGAACCC
1 TAAACCC
*
323 TGAACCC
1 TAAACCC
*
330 CAAACCC
1 TAAACCC
*
337 CAAACCC
1 TAAACCC
*
344 CAAACCC
1 TAAACCC
*
351 CAAACCC
1 TAAACCC
*
358 CAAACCC
1 TAAACCC
*
365 CAAACCC
1 TAAACCC
*
372 CAAACCC
1 TAAACCC
*
379 CAAACCC
1 TAAACCC
*
386 CAAACCC
1 TAAACCC
*
393 CAAACCC
1 TAAACCC
*
400 CAAACCC
1 TAAACCC
*
407 CAAACCC
1 TAAACCC
*
414 CAAACCC
1 TAAACCC
*
421 CAAACCC
1 TAAACCC
*
428 CAAACCC
1 TAAACCC
*
435 CAAACCC
1 TAAACCC
*
442 CAAACCC
1 TAAACCC
*
449 CAAACCC
1 TAAACCC
*
456 CAAACCC
1 TAAACCC
*
463 CAAACCC
1 TAAACCC
*
470 CAAACCC
1 TAAACCC
477 TAAACCC
1 TAAACCC
484 TAAACCC
1 TAAACCC
491 TAAACCC
1 TAAACCC
498 TAAACCC
1 TAAACCC
505 TAAACCC
1 TAAACCC
512 TAAACCC
1 TAAACCC
519 TAAACCC
1 TAAACCC
*
526 TCAACCC
1 TAAACCC
*
533 TCAACCC
1 TAAACCC
*
540 TCAACCC
1 TAAACCC
*
547 TCAACCC
1 TAAACCC
*
554 TCAACCC
1 TAAACCC
*
561 TCAACCC
1 TAAACCC
*
568 TCAACCC
1 TAAACCC
*
575 TCAACCC
1 TAAACCC
*
582 TCAACCC
1 TAAACCC
*
589 TCAACCC
1 TAAACCC
*
596 TCAACCC
1 TAAACCC
*
603 TCAACCC
1 TAAACCC
*
610 TCAACCC
1 TAAACCC
*
617 TCAACCC
1 TAAACCC
*
624 TCAACCC
1 TAAACCC
*
631 TCAACCC
1 TAAACCC
*
638 TCAACCC
1 TAAACCC
*
645 TCAACCC
1 TAAACCC
*
652 TCAACCC
1 TAAACCC
*
659 TCAACCC
1 TAAACCC
*
666 TCAACCC
1 TAAACCC
*
673 TCAACCC
1 TAAACCC
680 TAAACCC
1 TAAACCC
687 TAAACCC
1 TAAACCC
694 TAAACCC
1 TAAACCC
*
701 TAAGCCC
1 TAAACCC
708 TAAACCC
1 TAAACCC
715 TAAACCC
1 TAAACCC
722 TAAACCC
1 TAAACCC
729 TAAACCC
1 TAAACCC
*
736 TGAACCC
1 TAAACCC
*
743 TGAACCC
1 TAAACCC
*
750 TGAACCC
1 TAAACCC
*
757 TGAACCC
1 TAAACCC
*
764 TGAACCC
1 TAAACCC
*
771 CAAACCC
1 TAAACCC
*
778 TGAACCC
1 TAAACCC
*
785 CAAACCC
1 TAAACCC
*
792 CAAACCC
1 TAAACCC
*
799 CAAACCC
1 TAAACCC
*
806 CAAACCC
1 TAAACCC
* *
813 CAACCCC
1 TAAACCC
820 TAAACCC
1 TAAACCC
*
827 CAAACCC
1 TAAACCC
**
834 CGAACCC
1 TAAACCC
*
841 CAAACCC
1 TAAACCC
*
848 CAAACCC
1 TAAACCC
855 TAAACCC
1 TAAACCC
*
862 TAAAACC
1 TAAACCC
869 TAAAACCC
1 T-AAACCC
**
877 TAGCCCC
1 TAAACCC
884 TAAAACCC
1 T-AAACCC
892 -AAACCC
1 TAAACCC
*
898 CAAATCCC
1 TAAA-CCC
906 -AAACCCC
1 TAAA-CCC
913 TAAACCCC
1 TAAA-CCC
* *
921 AAAACCA
1 TAAACCC
*
928 TGAACCC
1 TAAACCC
*
935 TCAACCC
1 TAAACCC
942 TAAACCC
1 TAAACCC
949 TAAACCC
1 TAAACCC
** *
956 TAGGCTC
1 TAAACCC
*
963 TAGACCC
1 TAAACCC
*
970 TAGACCC
1 TAAACCC
977 TAAACCC
1 TAAACCC
* *
984 AAAACCT
1 TAAACCC
* *
991 TAAGCTC
1 TAAACCC
*
998 TAAAACCA
1 T-AAACCC
*
1006 TAGACCC
1 TAAACCC
***
1013 TAAAATTA
1 T-AAACCC
*
1021 TAAACAC
1 TAAACCC
1028 TAAACCC
1 TAAACCC
1035 TAAAACCC
1 T-AAACCC
* *
1043 TAATCTC
1 TAAACCC
*
1050 TAACCCC
1 TAAACCC
* *
1057 CAAACCT
1 TAAACCC
1064 TAAACCC
1 TAAACCC
1071 TAAAC
1 TAAAC
1076 ATTAAATAAA
Statistics
Matches: 986, Mismatches: 72, Indels: 20
0.91 0.07 0.02
Matches are distributed among these distances:
6 11 0.01
7 931 0.94
8 44 0.04
ACGTcount: A:0.38, C:0.47, G:0.03, T:0.12
Consensus pattern (7 bp):
TAAACCC
Found at i:2492 original size:21 final size:21
Alignment explanation
Indices: 2459--2517 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2449 GTCCATACAT
2459 ACAAAAA-ATCTGAACCGG-CC
1 ACAAAAACA-CTGAACCGGACC
* *
2479 ACTAAAACAACTGAACCGGACT
1 ACAAAAAC-ACTGAACCGGACC
2501 ACAAAAACACTGAACCG
1 ACAAAAACACTGAACCG
2518 AAACGGGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 6 0.18
21 18 0.55
22 9 0.27
ACGTcount: A:0.47, C:0.29, G:0.14, T:0.10
Consensus pattern (21 bp):
ACAAAAACACTGAACCGGACC
Found at i:3395 original size:96 final size:96
Alignment explanation
Indices: 3231--3428 Score: 315
Period size: 96 Copynumber: 2.1 Consensus size: 96
3221 AGAAGAAAAT
* *
3231 GCAGGATATCCGAGGAATAACTTAATCTAAGAAGGAATAGTAGCGGAATATGACAGGGATAAATC
1 GCAGGATATCCGAAGAATAACTTAATCTAAGAAGGAATAGTAGCGGAATATGACAGGAATAAATC
* *
3296 CGGAGAGGAATAGGACAGAAAATTAACTATA
66 CGGAGAGGAATAGGACAGAAAATTAACAACA
* * **
3327 GCAGGATATCCTAAGAATAACTTAATCTGAGAAGGAATAGTCTCGGAATATGACAGGAATAAATC
1 GCAGGATATCCGAAGAATAACTTAATCTAAGAAGGAATAGTAGCGGAATATGACAGGAATAAATC
*
3392 CGGAGAGGAATAGGATAGAAAATTAACAACA
66 CGGAGAGGAATAGGACAGAAAATTAACAACA
3423 GCAGGA
1 GCAGGA
3429 CAGTTAAAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (96 bp):
GCAGGATATCCGAAGAATAACTTAATCTAAGAAGGAATAGTAGCGGAATATGACAGGAATAAATC
CGGAGAGGAATAGGACAGAAAATTAACAACA
Found at i:9970 original size:16 final size:16
Alignment explanation
Indices: 9949--9983 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
9939 AGTCCTCGTA
9949 ATTTTA-TCACTTTAAC
1 ATTTTAGTC-CTTTAAC
9965 ATTTTAGTCCTTTAAC
1 ATTTTAGTCCTTTAAC
9981 ATT
1 ATT
9984 AAAATTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTTAGTCCTTTAAC
Found at i:18093 original size:11 final size:11
Alignment explanation
Indices: 18079--18126 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
18069 GTTTTCTCCC
18079 TATTTTGCTAT
1 TATTTTGCTAT
*
18090 TATTTTACTAT
1 TATTTTGCTAT
* *
18101 TATGTTGCTAC
1 TATTTTGCTAT
*
18112 TATTTTGTTAT
1 TATTTTGCTAT
18123 TATT
1 TATT
18127 GTTTGCATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.62
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:19306 original size:29 final size:29
Alignment explanation
Indices: 19268--19352 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
19258 AACATTTGTT
* *
19268 AATATGCATTAATTAAAACAAATATATAA
1 AATATACATTAATTATAACAAATATATAA
* *
19297 AATATACATTAATTATACCAAATGTATAA
1 AATATACATTAATTATAACAAATATATAA
* *
19326 AACATACATTAGTTATAACAAATATAT
1 AATATACATTAATTATAACAAATATAT
19353 TATTATTTGG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (29 bp):
AATATACATTAATTATAACAAATATATAA
Found at i:20809 original size:66 final size:66
Alignment explanation
Indices: 20733--20937 Score: 374
Period size: 66 Copynumber: 3.1 Consensus size: 66
20723 AAAGAAAAAG
*
20733 AAAAAAGAATATACAATTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACA
1 AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACA
20798 A
66 A
*
20799 AAAAAAGAATATACATTTTATTGTTTACTAATACTATTTCCATTATTTAGTTATTAATATCTACA
1 AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTAC-
20864 AA
65 AA
*
20866 AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGCTATTAATATCTACA
1 AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACA
20931 A
66 A
20932 AAAAAA
1 AAAAAA
20938 AAGAAAAAAG
Statistics
Matches: 134, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 70 0.52
67 64 0.48
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.42
Consensus pattern (66 bp):
AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACA
A
Found at i:20904 original size:67 final size:67
Alignment explanation
Indices: 20733--20938 Score: 378
Period size: 67 Copynumber: 3.1 Consensus size: 67
20723 AAAGAAAAAG
*
20733 AAAAAAGAATATACAATTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTAC-
1 AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACA
20797 AA
66 AA
*
20799 AAAAAAGAATATACATTTTATTGTTTACTAATACTATTTCCATTATTTAGTTATTAATATCTACA
1 AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACA
20864 AA
66 AA
*
20866 AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGCTATTAATATCTACA
1 AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACA
20931 AA
66 AA
20933 AAAAAA
1 AAAAAA
20939 AGAAAAAAGA
Statistics
Matches: 135, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 62 0.46
67 73 0.54
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (67 bp):
AAAAAAGAATATACATTTTATTGTTTACTAATATTATTTCCATTATTTAGTTATTAATATCTACA
AA
Found at i:39266 original size:24 final size:24
Alignment explanation
Indices: 39239--39334 Score: 65
Period size: 24 Copynumber: 4.2 Consensus size: 24
39229 CCTAGCCACC
**
39239 CACACCCACACACTTGCACTCACT
1 CACACCCACACACACGCACTCACT
** *
39263 CACATGCACACACACGCACTCGCT
1 CACACCCACACACACGCACTCACT
* * * *
39287 CACA--TATACACATGCA-T-ACA
1 CACACCCACACACACGCACTCACT
* *
39307 CACACACACACACACACACTCACT
1 CACACCCACACACACGCACTCACT
39331 CACA
1 CACA
39335 TGCACACATG
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
20 5 0.09
21 1 0.02
22 17 0.32
23 1 0.02
24 29 0.55
ACGTcount: A:0.36, C:0.45, G:0.05, T:0.14
Consensus pattern (24 bp):
CACACCCACACACACGCACTCACT
Found at i:39321 original size:44 final size:44
Alignment explanation
Indices: 39269--39355 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
39259 CACTCACATG
* * *
39269 CACACACACGCACTCGCTCACATATACACATGCATACACACACA
1 CACACACACACACTCACTCACATACACACATGCATACACACACA
* *
39313 CACACACACACACTCACTCACATGCACACATGCATGCACACAC
1 CACACACACACACTCACTCACATACACACATGCATACACACAC
39356 TCATTTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.38, C:0.43, G:0.07, T:0.13
Consensus pattern (44 bp):
CACACACACACACTCACTCACATACACACATGCATACACACACA
Found at i:40365 original size:54 final size:54
Alignment explanation
Indices: 40298--40400 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
40288 AATATACCTA
* * *
40298 TTTCATCGCAATCAGAGGCTATGAATGTTGATAATCAGGTAATATGAACAATCT
1 TTTCATCGCAATCAGAGGATATGAATGTTGAGAATCAGGTAACATGAACAATCT
* * *
40352 TTTCATCTCAATCAGAGTATATGGATGTTGAGAATCAGGTAACATGAAC
1 TTTCATCGCAATCAGAGGATATGAATGTTGAGAATCAGGTAACATGAAC
40401 TTTCTTCCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (54 bp):
TTTCATCGCAATCAGAGGATATGAATGTTGAGAATCAGGTAACATGAACAATCT
Found at i:43268 original size:27 final size:28
Alignment explanation
Indices: 43238--43296 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
43228 GGACTTTGGA
*
43238 ATTTATAATATAAAAA-TATATAAATTT
1 ATTTATAATAAAAAAATTATATAAATTT
* *
43265 ATTT-TTATAAAAAAATTGTATAAATTT
1 ATTTATAATAAAAAAATTATATAAATTT
*
43292 TTTTA
1 ATTTA
43297 ATTTTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
ATTTATAATAAAAAAATTATATAAATTT
Found at i:43508 original size:23 final size:24
Alignment explanation
Indices: 43477--43521 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
43467 TCTACTTTAA
*
43477 AATTGTTAA-AAAAATATTAAAGC
1 AATTATTAAGAAAAATATTAAAGC
*
43500 AATTATTAAGAAAAGTATTAAA
1 AATTATTAAGAAAAATATTAAA
43522 AATACCAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (24 bp):
AATTATTAAGAAAAATATTAAAGC
Found at i:46369 original size:19 final size:20
Alignment explanation
Indices: 46345--46395 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 20
46335 TTACAAAAAG
46345 AAATTCAAAATAATTTT-T-A
1 AAATTCAAAAT-ATTTTATAA
46364 AAATTCAAAATATTTTATAA
1 AAATTCAAAATATTTTATAA
46384 AAATTTCAAAAT
1 AAA-TTCAAAAT
46396 TTATATATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.17
19 12 0.41
20 4 0.14
21 8 0.28
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATTCAAAATATTTTATAA
Found at i:46402 original size:20 final size:20
Alignment explanation
Indices: 46345--46402 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
46335 TTACAAAAAG
*
46345 AAATTCAAAATAATT-T-TTA
1 AAATTCAAAAT-ATTATATAA
*
46364 AAATTCAAAATATTTTATAA
1 AAATTCAAAATATTATATAA
46384 AAATTTCAAAAT-TTATATA
1 AAA-TTCAAAATATTATATA
46403 TCTTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 3 0.09
19 12 0.35
20 11 0.32
21 8 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTCAAAATATTATATAA
Found at i:50304 original size:4 final size:4
Alignment explanation
Indices: 50295--50330 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
50285 TTGCTAGCTC
50295 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
50331 ATATTCTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CTAT
Found at i:79207 original size:50 final size:50
Alignment explanation
Indices: 79086--79334 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
79076 GATAATAACA
* * * ** * *
79086 TGCCAAAGCCATGTCCCAGATATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
79137 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
79187 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
79237 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
79292 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
79335 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:79263 original size:100 final size:104
Alignment explanation
Indices: 79085--79334 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
79075 TGATAATAAC
* **
79085 ATGCCAAAGCCATGTCCCAGATATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
79150 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
79187 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
79250 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
79292 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
79335 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:79450 original size:13 final size:13
Alignment explanation
Indices: 79429--79460 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
79419 GCTTGGATCA
*
79429 TCATCAAATAAAT
1 TCATAAAATAAAT
79442 TCATAAAATAAAT
1 TCATAAAATAAAT
79455 TCATAA
1 TCATAA
79461 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:79705 original size:29 final size:30
Alignment explanation
Indices: 79672--79728 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
79662 CCTCGACTCT
*
79672 AACTTTTTCA-AATTACAATTTTGCCCCTA
1 AACTTTTACATAATTACAATTTTGCCCCTA
*
79701 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACATAATTACAATTTTGCCCC
79729 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.42
Consensus pattern (30 bp):
AACTTTTACATAATTACAATTTTGCCCCTA
Found at i:81818 original size:23 final size:22
Alignment explanation
Indices: 81766--81818 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
81756 TCCACGTCTT
*
81766 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
81788 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
81811 TTTCTTTT
1 TTTCTTTT
81819 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:81843 original size:27 final size:27
Alignment explanation
Indices: 81813--81864 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
81803 TTCTTCAATT
81813 TCTTTTTCACTCTCAATCTCTTTTTGC
1 TCTTTTTCACTCTCAATCTCTTTTTGC
* **
81840 TCTTTTTCATTCTCTTTCTCTTTTT
1 TCTTTTTCACTCTCAATCTCTTTTT
81865 CCTCACTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.08, C:0.27, G:0.02, T:0.63
Consensus pattern (27 bp):
TCTTTTTCACTCTCAATCTCTTTTTGC
Found at i:85216 original size:4 final size:4
Alignment explanation
Indices: 85207--85235 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
85197 AGAAAAGGTA
85207 TAGC TAGC TAGC TAGC TAGC TAGC TAGC T
1 TAGC TAGC TAGC TAGC TAGC TAGC TAGC T
85236 CTAAAACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (4 bp):
TAGC
Found at i:88983 original size:5 final size:5
Alignment explanation
Indices: 88973--89005 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
88963 AAACAACTCT
88973 TTGTC TTGTC TTGTC TTGTC TTGTC TTGGTC TT
1 TTGTC TTGTC TTGTC TTGTC TTGTC TT-GTC TT
89006 TAAGTAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.18, G:0.21, T:0.61
Consensus pattern (5 bp):
TTGTC
Found at i:108015 original size:69 final size:69
Alignment explanation
Indices: 107861--108108 Score: 282
Period size: 69 Copynumber: 3.6 Consensus size: 69
107851 AGGGGTACCT
* ** * *
107861 GGAACAGAATCAGCAAAAATAGACGAGGTT-TGCCCCTTGAACAACTTATCCGCATAGACAGGAG
1 GGAACAGAATCAGCAAAAATAGACGA-GTTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAG
*
107925 AGCTT
65 AGCTA
* * * * * * * *
107930 GGAATAGATTCTGCAAATATGGCCGAATTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGT
1 GGAACAGAATCAGCAAAAATAGACGAGTTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGA
107995 GCTA
66 GCTA
* * *
107999 GGAACAGAATCAGCAAAAATAGATGAGCTCTTTCCCTTGAACATGTTATCTGCATAGGCAGGAGA
1 GGAACAGAATCAGCAAAAATAGACGAGTTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGA
**
108064 ATTA
66 GCTA
* * *
108068 GGAACAGAATCTGCAAAAATAGATGAGCTCTTCCCCTTGAA
1 GGAACAGAATCAGCAAAAATAGACGAGTTCTTCCCCTTGAA
108109 GACTTTGTTT
Statistics
Matches: 149, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
68 2 0.01
69 147 0.99
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (69 bp):
GGAACAGAATCAGCAAAAATAGACGAGTTCTTCCCCTTGAACATGTTATCTGCATAGGCAGGAGA
GCTA
Found at i:108100 original size:138 final size:137
Alignment explanation
Indices: 107861--108182 Score: 335
Period size: 138 Copynumber: 2.3 Consensus size: 137
107851 AGGGGTACCT
* * **
107861 GGAACAGAATCAGCAAAAATAGACGAGGTTTGCCCCTTGAACAACTTATCCGCATAGACAGGAGA
1 GGAACAGAATCAGCAAAAATAGACGAGCTTT-TCCCTTGAACATGTTATCCGCATAGACAGGAGA
* * * * * * * *
107926 GCTTGGAATAGATTCTGCAAATATGGCCGAATTCTTCCCCTTGAACA-TGTTATCTGCATAGGCA
65 GATTGGAACAGAATCTGCAAAAATAGACGAACTCTTCCCCTTGAACACT-TTATCTGCATAAGCA
107990 GGAG-TGCTA
129 GG-GCTGCTA
* * *
107999 GGAACAGAATCAGCAAAAATAGATGAGCTCTTTCCCTTGAACATGTTATCTGCATAGGCAGGAGA
1 GGAACAGAATCAGCAAAAATAGACGAGCT-TTTCCCTTGAACATGTTATCCGCATAGACAGGAGA
* * * * * **
108064 -ATTAGGAACAGAATCTGCAAAAATAGATGAGCTCTTCCCCTTGAAGACTTTGTTTTTATAAGCA
65 GATT-GGAACAGAATCTGCAAAAATAGACGAACTCTTCCCCTTGAACACTTTATCTGCATAAGCA
*
108128 GGGCTGCTT
129 GGGCTGCTA
* * *
108137 GGAATAGAATCCGCAAAAATAGACGAGCTTTTCCCGTGGAACATGT
1 GGAACAGAATCAGCAAAAATAGACGAGCTTTTCCC-TTGAACATGT
108183 CACCTATCTA
Statistics
Matches: 152, Mismatches: 27, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
137 9 0.06
138 140 0.92
139 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (137 bp):
GGAACAGAATCAGCAAAAATAGACGAGCTTTTCCCTTGAACATGTTATCCGCATAGACAGGAGAG
ATTGGAACAGAATCTGCAAAAATAGACGAACTCTTCCCCTTGAACACTTTATCTGCATAAGCAGG
GCTGCTA
Found at i:114121 original size:4 final size:4
Alignment explanation
Indices: 114112--114138 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
114102 CCTACTATTA
114112 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
114139 ATGGATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:117023 original size:6 final size:6
Alignment explanation
Indices: 117014--117056 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
117004 GAAGGCGAGT
* *
117014 GTGAGG GTGAGG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG G
1 GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG G
117057 AGGAGATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.28, C:0.00, G:0.56, T:0.16
Consensus pattern (6 bp):
GTGAAG
Found at i:117066 original size:18 final size:18
Alignment explanation
Indices: 117027--117067 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
117017 AGGGTGAGGG
* *
117027 TGAAGGTGAAGGTGAAGG
1 TGAAGGTGAAGGAGAAGA
*
117045 TGAAGGTGAAGGAGGAGA
1 TGAAGGTGAAGGAGAAGA
117063 TGAAG
1 TGAAG
117068 AGGAAGAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.15
Consensus pattern (18 bp):
TGAAGGTGAAGGAGAAGA
Found at i:130490 original size:52 final size:52
Alignment explanation
Indices: 130434--130717 Score: 128
Period size: 52 Copynumber: 5.1 Consensus size: 52
130424 TTTACAGTAC
130434 ATATATTTGATTGAGTATTATATAAGAATATTATTTTAAGAATTTTTAAATT
1 ATATATTTGATTGAGTATTATATAAGAATATTATTTTAAGAATTTTTAAATT
* * ** * * * ** *
130486 ATATAGTTAATT-AAAATATATTTAATAATATTATGTTAATTTATATTTTACAGTATC
1 ATATATTTGATTGAGTAT-TATATAAGAATATTATTTTAA-GAAT-TTTTA-A--ATT
130543 ATATATTATGATTTGAGTAAATTAATATAAGAA-ATTATTATTAAGAATTTTTTAAATT
1 ATATATT-TGA-TTGAGT--ATT-ATATAAGAATATTATT-TTAAGAA-TTTTTAAATT
* * * * * * ** *
130601 AT-TAGTTTAATTAAATA-TATTTAATAATATTATGTTAATTTATATTTTACAGTATC
1 ATATA-TTTGATTGAGTATTATATAAGAATATTATTTTAA-GAAT-TTTTA-A--ATT
* *
130657 ATATATTTAGATTTGAGTAAATAATATAAGAATATAATTATTAA-AATTTTTAAATT
1 ATATATTT-GA-TTGAGT--ATTATATAAGAATATTATT-TTAAGAATTTTTAAATT
130713 ATATA
1 ATATA
130718 GTTTAATTAA
Statistics
Matches: 165, Mismatches: 39, Indels: 52
0.64 0.15 0.20
Matches are distributed among these distances:
51 3 0.02
52 40 0.24
53 14 0.08
54 7 0.04
55 1 0.01
56 18 0.11
57 15 0.09
58 13 0.08
59 7 0.04
60 5 0.03
61 24 0.15
62 18 0.11
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.48
Consensus pattern (52 bp):
ATATATTTGATTGAGTATTATATAAGAATATTATTTTAAGAATTTTTAAATT
Found at i:130717 original size:56 final size:56
Alignment explanation
Indices: 130543--130837 Score: 154
Period size: 56 Copynumber: 5.2 Consensus size: 56
130533 TTACAGTATC
*
130543 ATATA-TTATGATTTGAGTAAATTAATATAAGAA-ATT-ATTATTAAGAATTTTTTAA-
1 ATATATTTA-GATTTGAGTAAA-TAATATAAGAATATTAATTATTAA-AATTTTTAAAT
* * * * * * *
130598 AT-TA-TTAG-TTTAATTAAATATATTTAATAATATTATGTTAATTTATA-TTTTACAGTAT
1 ATATATTTAGATTTGAGTAAATA-ATATAAGAATATTA-ATT-ATTAAAATTTTTA-A--AT
130656 CATATATTTAGATTTGAGTAAATAATATAAGAATA-TAATTATTAAAATTTTTAAATT
1 -ATATATTTAGATTTGAGTAAATAATATAAGAATATTAATTATTAAAATTTTTAAA-T
* * * * * *
130713 ATATAGTTTA-A-TT-A--AAATATATTTAATAATAATTATGTTATTTATA-TTTTACAGT
1 ATATA-TTTAGATTTGAGTAAATA-ATATAAGAAT-ATTA-ATTATTAAAATTTTTA-AAT
130768 ATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTAAAT
1 AT-ATAT-TTA-GATTTGAGTAAA-TAATATAAGAATATTAATTATTAA-AA-TTTTTAAAT
130830 A-ATATTTA
1 ATATATTTA
130838 ATTAAAATAT
Statistics
Matches: 180, Mismatches: 27, Indels: 62
0.67 0.10 0.23
Matches are distributed among these distances:
51 2 0.01
52 20 0.11
53 12 0.07
54 11 0.06
55 19 0.11
56 25 0.14
57 6 0.03
58 7 0.04
59 14 0.08
60 15 0.08
61 18 0.10
62 24 0.13
63 7 0.04
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (56 bp):
ATATATTTAGATTTGAGTAAATAATATAAGAATATTAATTATTAAAATTTTTAAAT
Found at i:130858 original size:114 final size:116
Alignment explanation
Indices: 130392--130859 Score: 740
Period size: 114 Copynumber: 4.1 Consensus size: 116
130382 ATTTCAAGTT
130392 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTA-CATATATTTGA-TTGAGT--ATT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTTGATTTGAGTAAATT
130453 -ATATAAGAATATTATT-TTAAGAATTTTTAAATTATATAG-TTAATTAAA
66 AATATAAGAATATTATTATTAAGAATTTTTAAATTATATAGTTTAATTAAA
130501 ATATATTTAATAAT-ATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATT-TGATTTGAGTAAAT
130565 TAATATAAGAA-ATTATTATTAAGAATTTTTTAAATTAT-TAGTTTAATT-AA
65 TAATATAAGAATATTATTATTAAGAA-TTTTTAAATTATATAGTTTAATTAAA
130615 ATATATTTAATAAT-ATTATGTTAATTTATATTTTACAGTATCATATATTTAGATTTGAGTAAA-
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTT-GATTTGAGTAAAT
*
130678 TAATATAAGAATATAATTATTAA-AATTTTTAAATTATATAGTTTAATTAAA
65 TAATATAAGAATATTATTATTAAGAATTTTTAAATTATATAGTTTAATTAAA
130729 ATATATTTAATAATAATTATGTT-ATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATT-TGATTTGAGTAAAT
130793 TAATATAAGAATATTAATTATTAAGAATTTTTTAAA-TA-ATA-TTTAATTAAA
65 TAATATAAGAATATT-ATTATTAAGAA-TTTTTAAATTATATAGTTTAATTAAA
130844 ATATA-TTAATAATAAT
1 ATATATTTAATAATAAT
130860 AAATATTAGT
Statistics
Matches: 338, Mismatches: 2, Indels: 33
0.91 0.01 0.09
Matches are distributed among these distances:
108 26 0.08
109 22 0.07
110 3 0.01
111 6 0.02
112 12 0.04
113 33 0.10
114 157 0.46
115 56 0.17
116 11 0.03
117 4 0.01
118 8 0.02
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (116 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTTGATTTGAGTAAATT
AATATAAGAATATTATTATTAAGAATTTTTAAATTATATAGTTTAATTAAA
Found at i:131140 original size:10 final size:10
Alignment explanation
Indices: 131127--131174 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
131117 TATTATAAAA
131127 TTTTATTTTT
1 TTTTATTTTT
*
131137 TTTTATTATT
1 TTTTATTTTT
131147 TTTTATTTTT
1 TTTTATTTTT
*
131157 TTTT-TTTAT
1 TTTTATTTTT
*
131166 TTATATTTT
1 TTTTATTTT
131175 GTTCATATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:131145 original size:13 final size:14
Alignment explanation
Indices: 131129--131174 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
131119 TTATAAAATT
131129 TTATTTTTT-TTTA
1 TTATTTTTTATTTA
131142 TTATTTTTTATTT-
1 TTATTTTTTATTTA
*
131155 TTTTTTTTTATTTA
1 TTATTTTTTATTTA
131169 -TATTTT
1 TTATTTT
131175 GTTCATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 26 0.90
14 3 0.10
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
TTATTTTTTATTTA
Found at i:131150 original size:20 final size:20
Alignment explanation
Indices: 131127--131167 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
131117 TATTATAAAA
131127 TTTTATTTTTTTTTATTATT
1 TTTTATTTTTTTTTATTATT
*
131147 TTTTATTTTTTTTTTTTATT
1 TTTTATTTTTTTTTATTATT
131167 T
1 T
131168 ATATTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (20 bp):
TTTTATTTTTTTTTATTATT
Found at i:131766 original size:119 final size:119
Alignment explanation
Indices: 131641--132277 Score: 722
Period size: 120 Copynumber: 5.3 Consensus size: 119
131631 ATACTACTTA
131641 ATAAAAAATAATAAATTC-TAATTATTATT-AATATATTCTTATATT-AACTATATAATTATCAA
1 ATAAAAAAT-ATAAATTCATAATTATTATTAAATATATT-TTA-ATTAAACTATATAATT-T-AA
131703 AAAAATTCTTAAATAA-TAATATTCTTATATTAATTTA-TCAAAT-ATAATATAAT-ATAC
61 AAAAATTCTT-AATAATTAATATTCTTATATTAATTTACTCAAATCATAATAT-ATGATAC
* *
131760 AAAAAAAAATATTAAAATATATATCATACATTAATTACTAAATATAATTTTAAAATTAAA-T-TC
1 -ATAAAAAATA-T---A-A-AT-TCATA-ATT-ATTATTAAATAT-ATTTT--AATTAAACTAT-
*
131823 ATAATTT--AAAAATTAATTAATAATTAATAATTCTTATATTAAATTTACTCAAATCATAATATA
52 ATAATTTAAAAAAATT-CTTAATAATTAAT-ATTCTTATATT-AATTTACTCAAATCATAATATA
131886 TGATAC
114 TGATAC
* *
131892 TGGTAAAAAATATAAATAACAT-ATTA-TATTAAATATATTTTAATTAAACTATATAATTTAAAA
1 --ATAAAAAATATAAAT-TCATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAA
131955 AAATTCTTAATAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATAC
63 AAATTCTTAATAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATAC
** *
132012 -T-GTAAATATAAATTAACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAA
1 ATAAAAAATATAAATT--CATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAA
132075 AATTCTTAATAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATAC
64 AATTCTTAATAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATAC
**
132131 -TGTAAAATATAAATTAACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT--AAA
1 ATAAAAAATATAAATT--CATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAA
132193 AATTCTTAATAA-TAATATTCTTATATTAATTTACTCAAATCATAATATATGATAC
64 AATTCTTAATAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATAC
**
132248 -TGTAAAATATAAATTAACATAATTA-TATTA
1 ATAAAAAATATAAATT--CATAATTATTATTA
132278 TTATAATTAT
Statistics
Matches: 468, Mismatches: 16, Indels: 70
0.84 0.03 0.13
Matches are distributed among these distances:
116 15 0.03
117 72 0.15
118 18 0.04
119 95 0.20
120 99 0.21
121 19 0.04
122 18 0.04
123 17 0.04
124 2 0.00
125 5 0.01
126 2 0.00
127 20 0.04
128 10 0.02
129 17 0.04
130 15 0.03
131 21 0.04
132 15 0.03
133 8 0.02
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (119 bp):
ATAAAAAATATAAATTCATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAA
TTCTTAATAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATAC
Found at i:131830 original size:19 final size:19
Alignment explanation
Indices: 131803--131847 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
131793 ATTACTAAAT
* *
131803 ATAATTTTAAAATTAAATTC
1 ATAATTTAAAAATT-AATTA
131823 ATAATTTAAAAATTAATTA
1 ATAATTTAAAAATTAATTA
131842 ATAATT
1 ATAATT
131848 AATAATTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATTTAAAAATTAATTA
Found at i:132001 original size:120 final size:120
Alignment explanation
Indices: 131659--132277 Score: 833
Period size: 119 Copynumber: 5.1 Consensus size: 120
131649 TAATAAATTC
131659 TAATTATTATT-AATATATTCTTATATT-AACTATATAATTATCAAAAAAATTCTTAAATAA-TA
1 TAATTATTATTAAATATATT-TTA-ATTAAACTATATAATT-T-AAAAAAATTCTT-AATAATTA
***
131721 ATATTCTTATATTAATTTA-TCAAAT-ATAATATAAT-ATACAAAAAAAAATATTAAAATATATA
61 ATATTCTTATATTAATTTACTCAAATCATAATAT-ATGATAC--TGTAAAATA-T-AAAT-TA-A
131783 TCA
119 -CA
* *
131786 TACATTAATTACTAAATATAATTTTAAAATTAAA-T-TCATAATTT--AAAAATTAATTAATAAT
1 TA-ATT-ATTATTAAATAT-ATTTT--AATTAAACTAT-ATAATTTAAAAAAATT-CTTAATAAT
131847 TAATAATTCTTATATTAAATTTACTCAAATCATAATATATGATACTGGTAAAAAATATAAA-TAA
59 TAAT-ATTCTTATATT-AATTTACTCAAATCATAATATATGATACT-GT--AAAATATAAATTAA
131911 CA
119 CA
131913 T-ATTA-TATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATT
1 TAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATT
131976 CTTATATTAATTTACTCAAATCATAATATATGATACTGT-AAATATAAATTAACA
66 CTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACA
*
132030 TAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAATATT
1 TAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATT
132095 CTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACA
66 CTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACA
132150 TAATTATTATTAAATATATTTTAATTAAACTATATAATTT--AAAAATTCTTAATAA-TAATATT
1 TAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATT
132212 CTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACA
66 CTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACA
132267 TAATTA-TATTA
1 TAATTATTATTA
132278 TTATAATTAT
Statistics
Matches: 457, Mismatches: 9, Indels: 63
0.86 0.02 0.12
Matches are distributed among these distances:
116 14 0.03
117 74 0.16
118 18 0.04
119 98 0.21
120 91 0.20
121 19 0.04
122 18 0.04
123 16 0.04
124 1 0.00
125 3 0.01
127 17 0.04
128 10 0.02
129 18 0.04
130 15 0.03
131 24 0.05
132 15 0.03
133 6 0.01
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (120 bp):
TAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATT
CTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACA
Found at i:132131 original size:239 final size:240
Alignment explanation
Indices: 131659--132285 Score: 840
Period size: 239 Copynumber: 2.6 Consensus size: 240
131649 TAATAAATTC
131659 TAATTATTATT-AATATATTCTTATATT-AACTATATAATTATCAAAAAAATTCTTAAATAATAA
1 TAATTATTATTAAATATATT-TTA-ATTAAACTATATAATT-T-AAAAAAATTCTT-AATAATAA
***
131722 TATTCTTATATTAATTTA-TCAAAT-ATAATATAAT-ATACAAAAAAAAATATTAAAATATATAT
61 TATTCTTATATTAATTTACTCAAATCATAATAT-ATGATAC---TGTAAATA-T-AAAT-TA-A-
*
131784 CATACATTAATTACTAAATATAATTTTAAAATTAAATTCATAATTTAAAAATTAATTAATAATTA
117 CATA-ATT-ATTATTAAATATAATTTT-AAATTAAATTCATAATTTAAAAATTAATTAATAATTA
131849 ATAATTCTTATATTAAATTTACTCAAATCATAATATATGATACTGGTAAAAAATATAAA-TAACA
179 ATAATTCTTATATTAAATTTACTCAAATCATAATATATGATACT-GT--AAAATATAAATTAACA
131913 T-ATTA-TATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATT
1 TAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAA-TAATATT
131976 CTTATATTAATTTACTCAAATCATAATATATGATACTGTAAATATAAATTAACATAATTATTATT
65 CTTATATTAATTTACTCAAATCATAATATATGATACTGTAAATATAAATTAACATAATTATTATT
*
132041 AAATAT-ATTTT-AATTAAACTAT-ATAATTTAATAAAATT-CTTAATAATTAAT-ATTCTTATA
130 AAATATAATTTTAAATTAAA-T-TCATAATTT-A-AAAATTAATTAATAATTAATAATTCTTATA
132101 TT-AATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACA
191 TTAAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACA
132150 TAATTATTATTAAATATATTTTAATTAAACTATATAATTT--AAAAATTCTTAATAATAATATTC
1 TAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATAATATTC
132213 TTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA-TATT
66 TTATATTAATTTACTCAAATCATAATATATGATACTGT-AAATATAAATTAACATAATTATTATT
*
132277 -ATTATAATT
130 AAATATAATT
132286 ATATAACTTG
Statistics
Matches: 352, Mismatches: 6, Indels: 48
0.87 0.01 0.12
Matches are distributed among these distances:
235 4 0.01
236 63 0.18
237 42 0.12
238 6 0.02
239 69 0.20
240 19 0.05
241 19 0.05
242 17 0.05
243 3 0.01
244 4 0.01
245 1 0.00
246 2 0.01
247 4 0.01
248 1 0.00
249 10 0.03
250 33 0.09
251 12 0.03
252 30 0.09
253 12 0.03
254 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (240 bp):
TAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATAATATTC
TTATATTAATTTACTCAAATCATAATATATGATACTGTAAATATAAATTAACATAATTATTATTA
AATATAATTTTAAATTAAATTCATAATTTAAAAATTAATTAATAATTAATAATTCTTATATTAAA
TTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACA
Found at i:137277 original size:45 final size:44
Alignment explanation
Indices: 137199--137287 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
137189 AAAATATGTC
*
137199 TATAGTGATTGTATTTTTGAAAATTTCAAAGTAGGAAATTTAATT
1 TATAGTGATTGTATTTTTAAAAATTTCAAAGTAGG-AATTTAATT
* *
137244 TATAGTGGTTGTATTTTTTAAAAATTT-ATAGTAGGAATTTAATT
1 TATAGTGATTGTA-TTTTTAAAAATTTCAAAGTAGGAATTTAATT
137288 CTGTGAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 9 0.22
45 19 0.47
46 12 0.30
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (44 bp):
TATAGTGATTGTATTTTTAAAAATTTCAAAGTAGGAATTTAATT
Found at i:137340 original size:25 final size:26
Alignment explanation
Indices: 137302--137350 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
137292 GAAGAATAAG
*
137302 TTTTATTATAAAAATCATGTTTAATT
1 TTTTATTATAAAAATCAAGTTTAATT
*
137328 TTTTATT-TCAAAATCAAGTTTAA
1 TTTTATTATAAAAATCAAGTTTAA
137351 GAATTGGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (26 bp):
TTTTATTATAAAAATCAAGTTTAATT
Found at i:137624 original size:23 final size:23
Alignment explanation
Indices: 137594--137639 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
137584 AGAAGCTAGT
137594 ATGTAACTTAATCAGGCAGCAGA
1 ATGTAACTTAATCAGGCAGCAGA
137617 ATGTAACTTAATCAGGCAGCAGA
1 ATGTAACTTAATCAGGCAGCAGA
137640 CATGAAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (23 bp):
ATGTAACTTAATCAGGCAGCAGA
Found at i:138373 original size:39 final size:39
Alignment explanation
Indices: 138306--138381 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
138296 TTCTTATATT
* *
138306 AAAATTCGAATCTAGCAGTCTTAAGTTTTAAGGTGTTTA
1 AAAATTCGAATCCAGCAATCTTAAGTTTTAAGGTGTTTA
* **
138345 AAAATTCGAATCCAGTAATCTTGTGTTTTAAGGTGTT
1 AAAATTCGAATCCAGCAATCTTAAGTTTTAAGGTGTT
138382 CAAGAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (39 bp):
AAAATTCGAATCCAGCAATCTTAAGTTTTAAGGTGTTTA
Found at i:141370 original size:22 final size:22
Alignment explanation
Indices: 141333--141399 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
141323 TTTTCCTTTC
141333 TTTATT-TATT-TCATTTACTTA
1 TTTATTATATTAT-ATTTACTTA
*
141354 TTTATTATATTATATTTA-TTT
1 TTTATTATATTATATTTACTTA
141375 TATTATTATATTATATATTTACTTA
1 T-TTATTATA-T-TATATTTACTTA
141400 AATATTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 9 0.24
22 17 0.45
23 2 0.05
24 8 0.21
25 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATTATATTATATTTACTTA
Found at i:141371 original size:14 final size:14
Alignment explanation
Indices: 141352--141390 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
141342 TTCATTTACT
141352 TATTTATTATATTA
1 TATTTATTATATTA
*
141366 TATTTATTTTATTA
1 TATTTATTATATTA
*
141380 T-TATATTATAT
1 TATTTATTATAT
141391 ATTTACTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTATTATATTA
Found at i:142395 original size:58 final size:58
Alignment explanation
Indices: 142245--142397 Score: 225
Period size: 58 Copynumber: 2.6 Consensus size: 58
142235 ATTCATCGGA
* * * *
142245 ATTAAACTCTAAACTTAACGCCAATTAACTTGAACTTACTAGCAATATCATTGACTCG
1 ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTTACCAGCAATATCATTGACTCG
* * * *
142303 ATTAAACTTTGAATTTAACGCCAATCAACTTGAATTTACCATCAATATGATTGACTCG
1 ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTTACCAGCAATATCATTGACTCG
*
142361 ATTAAACTCTGAACTTAATGCCAATCAACTTGAATTT
1 ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTT
142398 TCCAATATCT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 84 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.33
Consensus pattern (58 bp):
ATTAAACTCTGAACTTAACGCCAATCAACTTGAATTTACCAGCAATATCATTGACTCG
Found at i:146426 original size:3 final size:3
Alignment explanation
Indices: 146420--146444 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
146410 ATTGTCTGGT
146420 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
146445 AAATCTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:146512 original size:15 final size:16
Alignment explanation
Indices: 146481--146513 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
146471 TGTTATCAAC
*
146481 TAGTTAGACATAAATT
1 TAGTTAGACAAAAATT
146497 TAGTTAGA-AAAAATT
1 TAGTTAGACAAAAATT
146512 TA
1 TA
146514 AAATTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (16 bp):
TAGTTAGACAAAAATT
Found at i:147619 original size:29 final size:30
Alignment explanation
Indices: 147567--147635 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
147557 AGCCTCTATC
*
147567 TTTATAATTTTTAAAGGATTAAAT-CAAATT
1 TTTATAATTTTTAAAGGATAAAATAC-AATT
* *
147597 TTTATTATTTTT-AGGGATAAAATACAA-T
1 TTTATAATTTTTAAAGGATAAAATACAATT
147625 TTTACTAATTT
1 TTTA-TAATTT
147636 AAAATTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 5 0.15
29 16 0.48
30 12 0.36
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (30 bp):
TTTATAATTTTTAAAGGATAAAATACAATT
Found at i:147987 original size:29 final size:29
Alignment explanation
Indices: 147935--147990 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
147925 TATAGAGACG
** * *
147935 GATTAATTTAGTCTTTTTATTATTAAATA
1 GATTAATTTAGTCACTGTAATATTAAATA
147964 GATTAATTTAGTCACTGTAATATTAAA
1 GATTAATTTAGTCACTGTAATATTAAA
147991 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (29 bp):
GATTAATTTAGTCACTGTAATATTAAATA
Found at i:170496 original size:4 final size:4
Alignment explanation
Indices: 170487--170551 Score: 72
Period size: 4 Copynumber: 17.8 Consensus size: 4
170477 CCCCATTCGT
170487 TTTC TTTC -TTC TTTC TTTC -TTC -TTC -TTC -TTC -TTC TTT- TATTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC
170529 TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTT
170552 TTTATTTTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
3 19 0.33
4 37 0.65
5 1 0.02
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:170551 original size:12 final size:11
Alignment explanation
Indices: 170487--170550 Score: 80
Period size: 11 Copynumber: 5.9 Consensus size: 11
170477 CCCCATTCGT
170487 TTTCTTTCTTC
1 TTTCTTTCTTC
170498 TTTCTTTCTTC
1 TTTCTTTCTTC
170509 -TTC-TTCTTC
1 TTTCTTTCTTC
*
170518 -TTCTTTTATTC
1 TTTC-TTTCTTC
170529 TTTCTTTCTTTC
1 TTTCTTTC-TTC
170541 TTTCTTTCTT
1 TTTCTTTCTT
170551 TTTTATTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
9 9 0.19
10 3 0.06
11 21 0.45
12 14 0.30
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTCTTTCTTC
Found at i:175884 original size:23 final size:23
Alignment explanation
Indices: 175857--175900 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
175847 GAAATTAAAT
* *
175857 TATAATTTTTATAATAATAAAAA
1 TATAAATTTTAAAATAATAAAAA
*
175880 TATAAATTTTAAAATATTAAA
1 TATAAATTTTAAAATAATAAA
175901 TTAAAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAAATTTTAAAATAATAAAAA
Found at i:175892 original size:15 final size:15
Alignment explanation
Indices: 175876--175911 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
175866 TATAATAATA
175876 AAAATA-TAAATTTT
1 AAAATATTAAATTTT
175890 AAAATATTAAA--TT
1 AAAATATTAAATTTT
175903 AAAATATTA
1 AAAATATTA
175912 TTATTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.52
14 6 0.29
15 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATTAAATTTT
Found at i:192110 original size:5 final size:5
Alignment explanation
Indices: 192102--192132 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
192092 TGAAACATTC
192102 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
192133 ATAGGGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:195945 original size:3 final size:3
Alignment explanation
Indices: 195937--195972 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
195927 GCCTTTAAGG
195937 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
195973 TTCTTTTGGT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:200672 original size:31 final size:31
Alignment explanation
Indices: 200637--200705 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
200627 TTTCAAAAAT
200637 AATTATTCAAAAAATTTTATTTAA-ATCACTA
1 AATTATTCAAAAAATTTTATTTAAGA-CACTA
*
200668 AATTATTTAAAAAATTTTATTTAAGACACTA
1 AATTATTCAAAAAATTTTATTTAAGACACTA
*
200699 AGTTATT
1 AATTATT
200706 AATTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (31 bp):
AATTATTCAAAAAATTTTATTTAAGACACTA
Found at i:215316 original size:2 final size:2
Alignment explanation
Indices: 215309--215334 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
215299 AGTTCACCTA
215309 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
215335 TCATCAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:222535 original size:26 final size:28
Alignment explanation
Indices: 222496--222547 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
222486 CAATATAGGC
*
222496 TTTTACAATATTATCATAA-TTTTTTCA
1 TTTTACAATATTATAATAACTTTTTTCA
*
222523 TTTTATAA-ATTATAATAACTTTTTT
1 TTTTACAATATTATAATAACTTTTTT
222548 TTTACCAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTTACAATATTATAATAACTTTTTTCA
Found at i:240064 original size:25 final size:25
Alignment explanation
Indices: 240025--240087 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
240015 CTAATTTCTC
* *
240025 CTTTCTTTCTT-TCCCTTTTTCTTTT
1 CTTTCTTT-TTCTCCCTGTTTCGTTT
240050 CTTTCTTTTTCTCCCTGTTTCGTTT
1 CTTTCTTTTTCTCCCTGTTTCGTTT
*
240075 CTATTCTATTTCT
1 CT-TTCTTTTTCT
240088 TTTATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 22 0.67
26 9 0.27
ACGTcount: A:0.03, C:0.27, G:0.03, T:0.67
Consensus pattern (25 bp):
CTTTCTTTTTCTCCCTGTTTCGTTT
Found at i:242326 original size:29 final size:30
Alignment explanation
Indices: 242283--242345 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
242273 TTCAAGACTC
* *
242283 AAATTTCATAATTCA-AAAA-AAAAGTACT
1 AAATTTAATAATTCATAAAATAAAAGAACT
*
242311 AAATTTAATCAATTCATAAAATATAAGAACT
1 AAATTTAAT-AATTCATAAAATAAAAGAACT
242342 AAAT
1 AAAT
242346 CCGCAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 8 0.28
29 6 0.21
30 4 0.14
31 11 0.38
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (30 bp):
AAATTTAATAATTCATAAAATAAAAGAACT
Found at i:252026 original size:7 final size:7
Alignment explanation
Indices: 252014--252071 Score: 116
Period size: 7 Copynumber: 8.3 Consensus size: 7
252004 TTGCCTTGCT
252014 TCAGGTC
1 TCAGGTC
252021 TCAGGTC
1 TCAGGTC
252028 TCAGGTC
1 TCAGGTC
252035 TCAGGTC
1 TCAGGTC
252042 TCAGGTC
1 TCAGGTC
252049 TCAGGTC
1 TCAGGTC
252056 TCAGGTC
1 TCAGGTC
252063 TCAGGTC
1 TCAGGTC
252070 TC
1 TC
252072 GAGACATAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.29
Consensus pattern (7 bp):
TCAGGTC
Found at i:253640 original size:8 final size:8
Alignment explanation
Indices: 253627--253661 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
253617 AAATAAATAT
253627 TAAAAAAA
1 TAAAAAAA
253635 TAAAAAAA
1 TAAAAAAA
*
253643 TATAAAAA
1 TAAAAAAA
253651 TAAAAGAAA
1 TAAAA-AAA
253660 TA
1 TA
253662 TTTAACTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 19 0.79
9 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (8 bp):
TAAAAAAA
Found at i:253643 original size:19 final size:17
Alignment explanation
Indices: 253616--253663 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 17
253606 TTAGATCCAT
*
253616 TAAATAAATATTAAAAAAA
1 TAAAAAAATATT--AAAAA
253635 TAAAAAAATA-TAAAAA
1 TAAAAAAATATTAAAAA
253651 TAAAAGAAATATT
1 TAAAA-AAATATT
253664 TAACTGTACC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.38
17 5 0.19
18 2 0.08
19 9 0.35
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (17 bp):
TAAAAAAATATTAAAAA
Found at i:253651 original size:16 final size:17
Alignment explanation
Indices: 253630--253662 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
253620 TAAATATTAA
253630 AAAAATAAAA-AAATAT
1 AAAAATAAAAGAAATAT
253646 AAAAATAAAAGAAATAT
1 AAAAATAAAAGAAATAT
253663 TTAACTGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAAAAGAAATAT
Found at i:253755 original size:115 final size:111
Alignment explanation
Indices: 253628--253871 Score: 258
Period size: 113 Copynumber: 2.1 Consensus size: 111
253618 AATAAATATT
* *
253628 AAAAAAATAAAAAAATATAAAAATAAAAGAAATATTTAA-CT-GTACCGGCCATTGGTAGGCCAC
1 AAAAAAATAAAAAAATATAAAAATAAAACAAA-A---AAGCTGGTACCGGCCATTGGCAGGCCAC
* * *
253691 CACCAAATTTTTTTTTTACTTTTTTCGTATATTGATACTTGCTATTGACACG
62 CACC-AA-TTTTTTTTTACTTTTTTCGTATACTGATACGTGATATTGACACG
***** ** * * *
253743 AAAAAAATAAAAAAAAATATTTCTTTCCACCAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCA
1 AAAAAAAT--AAAAAAATATAAAAATAAAACAAAAAAGCTGGTACCGGCCATTGGCAGGCCACCA
253808 CCAATTTTTTTTTACTTTTTTCGTATACTGATACGTGATATTGACACG
64 CCAATTTTTTTTTACTTTTTTCGTATACTGATACGTGATATTGACACG
253856 AAAAAAAGTAAAAAAA
1 AAAAAAA-TAAAAAAA
253872 AAATTACTAT
Statistics
Matches: 109, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
112 7 0.06
113 50 0.46
114 4 0.04
115 32 0.29
116 1 0.01
117 15 0.14
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.31
Consensus pattern (111 bp):
AAAAAAATAAAAAAATATAAAAATAAAACAAAAAAGCTGGTACCGGCCATTGGCAGGCCACCACC
AATTTTTTTTTACTTTTTTCGTATACTGATACGTGATATTGACACG
Found at i:254007 original size:58 final size:60
Alignment explanation
Indices: 253917--254042 Score: 175
Period size: 59 Copynumber: 2.1 Consensus size: 60
253907 AAAACTCGAA
* * **
253917 TTTTTTTACTGTACTAGGCGCCGGCCATTGACAGGCTAGCA-CCTAAATTTTTTTTTCCT
1 TTTTTTTTCTGTACTAGGCGCCGGCCATTGACAGGCCAGCAGCAAAAATTTTTTTTTCCT
* *
253976 TTTTTTTTC-GTACTGGGTGCCGGCCATTGACAGGCCAGCAGCAAAAATTTTTTTTTCCT
1 TTTTTTTTCTGTACTAGGCGCCGGCCATTGACAGGCCAGCAGCAAAAATTTTTTTTTCCT
*
254035 TCTTTTTT
1 TTTTTTTT
254043 GTATATCAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 28 0.47
59 31 0.53
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (60 bp):
TTTTTTTTCTGTACTAGGCGCCGGCCATTGACAGGCCAGCAGCAAAAATTTTTTTTTCCT
Found at i:257509 original size:17 final size:17
Alignment explanation
Indices: 257487--257525 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
257477 ACTTTCATAA
257487 TATTATTCGT-ATAACAT
1 TATTATTC-TAATAACAT
257504 TATTATTCTAATAACAT
1 TATTATTCTAATAACAT
257521 T-TTAT
1 TATTAT
257526 CGTTTTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (17 bp):
TATTATTCTAATAACAT
Found at i:257571 original size:12 final size:12
Alignment explanation
Indices: 257554--257578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
257544 CAGGATAGTG
257554 AAAATTATGAAC
1 AAAATTATGAAC
257566 AAAATTATGAAC
1 AAAATTATGAAC
257578 A
1 A
257579 GTTTCAAACT
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:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATTATGAAC
Found at i:258952 original size:17 final size:17
Alignment explanation
Indices: 258926--258961 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
258916 AAATCCCTAA
* *
258926 CCCCTGACCCTTAAATC
1 CCCCTAACCCCTAAATC
258943 CCCCTAACCCCTAAATC
1 CCCCTAACCCCTAAATC
258960 CC
1 CC
258962 TAATCCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.53, G:0.03, T:0.19
Consensus pattern (17 bp):
CCCCTAACCCCTAAATC
Found at i:260006 original size:82 final size:82
Alignment explanation
Indices: 259911--260094 Score: 192
Period size: 82 Copynumber: 2.2 Consensus size: 82
259901 GCGCTTCAAC
* * ** * * *
259911 AAAAACGTCGCTAAAACCCCTAACACTAGCGGCGTTTCTAA-AAAAACGACTCTAAAAATCTTAA
1 AAAAACGCCGCTAAAACCCCAAACACTAGCAACGCTT-TAACAAAAACGACGCTAAAAACCTTAA
*
259975 CTTTAGCGGCGCTT-ATTT
65 CGTTAGCGGCGCTTGA-TT
** * * * *
259993 AAAAACGCCGCTAAAAGGCCAAACATTAGCAACGCTTTAACGAAAACGCCGCTAAATACCTTAAC
1 AAAAACGCCGCTAAAACCCCAAACACTAGCAACGCTTTAACAAAAACGACGCTAAAAACCTTAAC
*
260058 GTTAGCGGCGGTTGATT
66 GTTAGCGGCGCTTGATT
*
260075 AAAAACGCCACTAAAACCCC
1 AAAAACGCCGCTAAAACCCC
260095 CGACCATTAG
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
81 3 0.04
82 78 0.95
83 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (82 bp):
AAAAACGCCGCTAAAACCCCAAACACTAGCAACGCTTTAACAAAAACGACGCTAAAAACCTTAAC
GTTAGCGGCGCTTGATT
Found at i:265079 original size:30 final size:30
Alignment explanation
Indices: 265045--265107 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
265035 ACTTAACAAC
265045 CAAATATCTCTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
* * *
265075 CAAATGTTTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
265105 CAA
1 CAA
265108 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.29
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:275714 original size:29 final size:28
Alignment explanation
Indices: 275611--275709 Score: 173
Period size: 28 Copynumber: 3.5 Consensus size: 28
275601 AAAAATAAAA
275611 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
275639 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
275667 ATTTACCAAAATATTTA-AACTTTTTTATT
1 ATTTACCAAAATA-TTACAACTTTTTT-TT
275696 ATTTACCAAAATAT
1 ATTTACCAAAATAT
275710 ATAAAAAAAC
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
28 51 0.74
29 18 0.26
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:275847 original size:27 final size:27
Alignment explanation
Indices: 275779--275849 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
275769 CCCCAATGGT
* *
275779 ATTGGCGGCACCAAAGGTGCCAAAATC
1 ATTGGCGGCACCAATGGTGCCAAAACC
*
275806 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAAAACC
275833 ATTGGCGGCACCAATGG
1 ATTGGCGGCACCAATGG
275850 GTTTTATGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAACC
Found at i:275914 original size:18 final size:19
Alignment explanation
Indices: 275887--276035 Score: 112
Period size: 20 Copynumber: 7.6 Consensus size: 19
275877 AGAAGAGAAA
275887 AAAGGA-AAGAAAGAAAGG
1 AAAGGAGAAGAAAGAAAGG
*
275905 AGAGGGAAGAAAGAAAGAAAGG
1 A-AAGG-AG-AAGAAAGAAAGG
*
275927 AGAGGA-AAGAAAGAAAAGG
1 AAAGGAGAAGAAAG-AAAGG
*
275946 AAAGGAGAAGAGAAAAAAGG
1 AAAGGAGAAGA-AAGAAAGG
*
275966 AAAGAAAGAAG-AAGAAAAGG
1 AAAG-GAGAAGAAAG-AAAGG
275986 AGAA-GAGAAGAAA-AAA-G
1 A-AAGGAGAAGAAAGAAAGG
*
276003 AAAGAAAGAAGGAAAGAAAGGG
1 AAAG-GAGAA-GAAAGAAA-GG
276025 AAAGGAGAAGA
1 AAAGGAGAAGA
276036 GAAAAAAAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
16 2 0.02
17 2 0.02
18 15 0.14
19 24 0.23
20 28 0.27
21 15 0.14
22 18 0.17
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
AAAGGAGAAGAAAGAAAGG
Found at i:275916 original size:22 final size:22
Alignment explanation
Indices: 275891--275973 Score: 103
Period size: 22 Copynumber: 3.6 Consensus size: 22
275881 GAGAAAAAAG
275891 GAAAGAAAGAAAGGAGAGGGAA
1 GAAAGAAAGAAAGGAGAGGGAA
*
275913 GAAAGAAAGAAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAGAGGGAA
*
275935 GAAAGAAAAGGAAAGGAGAAGAGAA
1 GAAAG-AAA-GAAAGGAG-AGGGAA
*
275960 AAAAGGAAAGAAAG
1 GAAA-GAAAGAAAG
275974 AAGAAGAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
22 26 0.49
23 3 0.06
24 13 0.25
25 10 0.19
26 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (22 bp):
GAAAGAAAGAAAGGAGAGGGAA
Found at i:275934 original size:14 final size:14
Alignment explanation
Indices: 275886--276022 Score: 85
Period size: 12 Copynumber: 10.0 Consensus size: 14
275876 CAGAAGAGAA
275886 AAAAGGAAAGAAAG
1 AAAAGGAAAGAAAG
* *
275900 -AAAGGAGAGGGAAG
1 AAAAGGA-AAGAAAG
275914 -AAA-GAAAGAAAG
1 AAAAGGAAAGAAAG
* *
275926 GAGAGGAAAGAAAG
1 AAAAGGAAAGAAAG
*
275940 AAAAGGAAAG-GAG
1 AAAAGGAAAGAAAG
*
275953 AAGA-GAAA-AAAG
1 AAAAGGAAAGAAAG
*
275965 GAAA-GAAAGAAGAAG
1 AAAAGGAAAG-A-AAG
275980 AAAAGGAGAAGAGAAG
1 AAAAGGA-AAGA-AAG
*
275996 AAAAAAGAAAGAAAG
1 -AAAAGGAAAGAAAG
276011 --AAGGAAAGAAAG
1 AAAAGGAAAGAAAG
276023 GGAAAGGAGA
Statistics
Matches: 98, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
12 28 0.29
13 15 0.15
14 26 0.27
15 9 0.09
16 11 0.11
17 9 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AAAAGGAAAGAAAG
Found at i:276054 original size:79 final size:80
Alignment explanation
Indices: 275877--276056 Score: 229
Period size: 79 Copynumber: 2.4 Consensus size: 80
275867 GTGGTGGGGC
* *
275877 AGAAGAGAAAAAAG---GAAAG-A-AAG-AAAGGAGAGGGAAGAAAGAAAGAAAGGAGAGGAAAG
1 AGAAGAGAAAAAAGAAAGAAAGAAGAAGAAAAGGAGAGAGAAGAAAGAAAGAAAGGAGAAGAAAG
275936 AAAGAAAAGGAAAGG
66 AAAGAAAAGGAAAGG
275951 AGAAGAGAAAAAAGGAAAGAAAGAAGAAGAAAAGGAGAAGAGAAGAAA-AAAGAAA-GA-AAGAA
1 AGAAGAGAAAAAA-GAAAGAAAGAAGAAGAAAAGGAG-AGAGAAGAAAGAAAGAAAGGAGAAGAA
* *
276013 GGAAAGAAAGGGAAAGG
64 AGAAAGAAAAGGAAAGG
276030 AGAAGAGAAAAAA-AAAG-AAGAAGAAGA
1 AGAAGAGAAAAAAGAAAGAAAGAAGAAGA
276057 GGGAAGAAAG
Statistics
Matches: 94, Mismatches: 4, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
74 13 0.14
75 1 0.01
76 10 0.11
77 4 0.04
78 5 0.05
79 33 0.35
80 5 0.05
81 14 0.15
82 9 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (80 bp):
AGAAGAGAAAAAAGAAAGAAAGAAGAAGAAAAGGAGAGAGAAGAAAGAAAGAAAGGAGAAGAAAG
AAAGAAAAGGAAAGG
Found at i:276067 original size:44 final size:44
Alignment explanation
Indices: 275877--276055 Score: 152
Period size: 44 Copynumber: 4.3 Consensus size: 44
275867 GTGGTGGGGC
* * *
275877 AGAAGAGAAAAAAGGAAAGAAA--GAAAGGAG-AGGGAAGAAAGAA
1 AGAA-AGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAA-AAAAAA
* * *
275920 AGAAAGGAGAGGAAAGAAAGAAAAGGAAAGGAGAAGAG--AAAAAA
1 AGAAA-GA-AAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
* *
275964 GGAAAGAAAGAA-G-AAG--A---AAAGGAGAAGAGAAGAAAAA
1 AGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
276001 AGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
1 AGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
276045 AG-AAG-AAGAAG
1 AGAAAGAAAGAAG
276056 AGGGAAGAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
35 12 0.11
37 16 0.14
38 2 0.02
39 3 0.03
40 3 0.03
41 2 0.02
42 11 0.10
43 11 0.10
44 41 0.37
46 8 0.07
47 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (44 bp):
AGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
Found at i:276175 original size:33 final size:35
Alignment explanation
Indices: 276138--276227 Score: 112
Period size: 37 Copynumber: 2.5 Consensus size: 35
276128 GTGTTTAAAA
*
276138 TTTATGTA-ATGTATA-TTATAGTTATTTTATTAT
1 TTTATGTACATATATATTTATAGTTATTTTATTAT
*
276171 TTTATTTAGCATATATATTTTATAGTTATTTTATTAT
1 TTTATGTA-CATATATA-TTTATAGTTATTTTATTAT
*
276208 TTTATTTAGCATATATATTT
1 TTTATGTA-CATATATATTT
276228 TATGAAATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.14
35 6 0.12
36 3 0.06
37 35 0.69
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (35 bp):
TTTATGTACATATATATTTATAGTTATTTTATTAT
Found at i:276178 original size:37 final size:37
Alignment explanation
Indices: 276149--276230 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
276139 TTATGTAATG
276149 TATATTATAGTTATTTTATTATTTTATTTAGCATATA
1 TATATTATAGTTATTTTATTATTTTATTTAGCATATA
*
276186 TATTTTATAGTTATTTTATTATTTTATTTAGCATATA
1 TATATTATAGTTATTTTATTATTTTATTTAGCATATA
*
276223 TATTTTAT
1 TATATTAT
276231 GAAATATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.62
Consensus pattern (37 bp):
TATATTATAGTTATTTTATTATTTTATTTAGCATATA
Found at i:276191 original size:18 final size:18
Alignment explanation
Indices: 276168--276230 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
276158 GTTATTTTAT
276168 TATTTTATTTAGCATATA
1 TATTTTATTTAGCATATA
***
276186 TATTTTATAGTTATTTTAT-
1 TATTTTAT--TTAGCATATA
276205 TATTTTATTTAGCATATA
1 TATTTTATTTAGCATATA
276223 TATTTTAT
1 TATTTTAT
276231 GAAATATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 6 0.17
18 16 0.44
19 8 0.22
20 6 0.17
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTTTATTTAGCATATA
Found at i:276761 original size:11 final size:11
Alignment explanation
Indices: 276747--276782 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
276737 TTCGGGTTAT
276747 TTACCAAAATA
1 TTACCAAAATA
* *
276758 TTACAAAAAAA
1 TTACCAAAATA
276769 TTACCAAAATA
1 TTACCAAAATA
276780 TTA
1 TTA
276783 TAAAGTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (11 bp):
TTACCAAAATA
Found at i:282460 original size:26 final size:26
Alignment explanation
Indices: 282411--282463 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
282401 ACACACTAAA
* *
282411 ATTATTAATTTTATACTACGAATAAT
1 ATTAATAATTTTATACTACAAATAAT
282437 ATTAATAATTTTATACT-CAAAATAAT
1 ATTAATAATTTTATACTAC-AAATAAT
282463 A
1 A
282464 CACACTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATAATTTTATACTACAAATAAT
Found at i:282657 original size:3 final size:3
Alignment explanation
Indices: 282649--282680 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
282639 TCTTCATACT
282649 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
282681 TAATAATAAT
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:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:282771 original size:19 final size:21
Alignment explanation
Indices: 282747--282785 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
282737 ACTACAACAA
*
282747 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAATAATATAC
282766 AAAATAATAACAATAATATA
1 AAAATAATAACAATAATATA
282786 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATAATAACAATAATATAC
Found at i:282875 original size:32 final size:33
Alignment explanation
Indices: 282839--282901 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
282829 CGCGCCAACT
282839 TTTC-TTTTTTTTTTGAATTTTCTCTCTTCTGC
1 TTTCTTTTTTTTTTTGAATTTTCTCTCTTCTGC
*
282871 TTTCTTTTTTTTTTTTGATTTTTCTCTCTTC
1 TTTC-TTTTTTTTTTTGAATTTTCTCTCTTC
282902 AGCTGGGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 4 0.14
34 24 0.86
ACGTcount: A:0.05, C:0.17, G:0.05, T:0.73
Consensus pattern (33 bp):
TTTCTTTTTTTTTTTGAATTTTCTCTCTTCTGC
Found at i:282965 original size:27 final size:27
Alignment explanation
Indices: 282928--283026 Score: 153
Period size: 27 Copynumber: 3.7 Consensus size: 27
282918 TATAAATAAT
*
282928 ACCAGTGGTGCCGCCAATGGTATTGGC
1 ACCATTGGTGCCGCCAATGGTATTGGC
* *
282955 ACAATTGGTGCCGCCAATAGTATTGGC
1 ACCATTGGTGCCGCCAATGGTATTGGC
*
282982 ACCATTGGTGCCGCCAATGGTTTTGGC
1 ACCATTGGTGCCGCCAATGGTATTGGC
*
283009 ACCTTTGGTGCCGCCAAT
1 ACCATTGGTGCCGCCAAT
283027 ACCATTGGGG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (27 bp):
ACCATTGGTGCCGCCAATGGTATTGGC
Found at i:283156 original size:28 final size:28
Alignment explanation
Indices: 283096--283195 Score: 157
Period size: 28 Copynumber: 3.5 Consensus size: 28
283086 GTTTTTTTAT
283096 ATATTTTGGTAAATAATAAAAAAAGTT-TAA
1 ATATTTTGGTAAAT-A-AAAAAAAGTTGT-A
*
283126 ATATTATGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
283154 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
283182 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
283196 TTTTATTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
28 52 0.78
29 2 0.03
30 13 0.19
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:286758 original size:8 final size:8
Alignment explanation
Indices: 286741--286771 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
286731 TTTTCATTGC
*
286741 ATTTTGTT
1 ATTTTATT
286749 ATTTTATT
1 ATTTTATT
286757 ATTTTATT
1 ATTTTATT
286765 ATTTTAT
1 ATTTTAT
286772 AGACATGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (8 bp):
ATTTTATT
Found at i:287160 original size:19 final size:20
Alignment explanation
Indices: 287145--287185 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
287135 GTTACAATAT
287145 AATAGT-AAAACAACAACAA
1 AATAGTGAAAACAACAACAA
*
287164 AATAGTGAAAACAACAGCAA
1 AATAGTGAAAACAACAACAA
287184 AA
1 AA
287186 AGTAGCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.66, C:0.15, G:0.10, T:0.10
Consensus pattern (20 bp):
AATAGTGAAAACAACAACAA
Found at i:292603 original size:18 final size:17
Alignment explanation
Indices: 292591--292624 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
292581 ATTTTTATTT
*
292591 ATTTTATATTTTTTAAAA
1 ATTTTA-ATTTTTTATAA
292609 ATTTTAATTTTTTATA
1 ATTTTAATTTTTTATA
292625 TTTGAACTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTAATTTTTTATAA
Found at i:302439 original size:11 final size:12
Alignment explanation
Indices: 302408--302438 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
302398 ACAATTTATC
302408 TTATTTTTGTAA
1 TTATTTTTGTAA
302420 TTATTTTTGTAA
1 TTATTTTTGTAA
302432 TTATTTT
1 TTATTTT
302439 GATTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTATTTTTGTAA
Found at i:308463 original size:72 final size:72
Alignment explanation
Indices: 308380--308525 Score: 283
Period size: 72 Copynumber: 2.0 Consensus size: 72
308370 CTGCAAGCAA
*
308380 GTAATGTTCTTGATTTGTCTTGTTTGATCATTATGTGGAAAATAAGGGCTTGACTGATGTTTGTG
1 GTAATGTTCTTGATTTGTCCTGTTTGATCATTATGTGGAAAATAAGGGCTTGACTGATGTTTGTG
308445 AAGAATT
66 AAGAATT
308452 GTAATGTTCTTGATTTGTCCTGTTTGATCATTATGTGGAAAATAAGGGCTTGACTGATGTTTGTG
1 GTAATGTTCTTGATTTGTCCTGTTTGATCATTATGTGGAAAATAAGGGCTTGACTGATGTTTGTG
308517 AAGAATT
66 AAGAATT
308524 GT
1 GT
308526 CTTATCACAC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (72 bp):
GTAATGTTCTTGATTTGTCCTGTTTGATCATTATGTGGAAAATAAGGGCTTGACTGATGTTTGTG
AAGAATT
Found at i:311394 original size:10 final size:10
Alignment explanation
Indices: 311374--311476 Score: 63
Period size: 10 Copynumber: 10.5 Consensus size: 10
311364 TTATTTATTC
311374 TTTAGAAATTT
1 TTTA-AAATTT
311385 TTTAAAATTT
1 TTTAAAATTT
** *
311395 TCCATAATTT
1 TTTAAAATTT
*
311405 TTTAAAA-TA
1 TTTAAAATTT
*
311414 TAT-AAA--T
1 TTTAAAATTT
*
311421 TTTGAAATTT
1 TTTAAAATTT
*
311431 TTTATAAATAT
1 TTTA-AAATTT
311442 TTT-AAATTT
1 TTTAAAATTT
*
311451 TTAAAAATTAT
1 TTTAAAATT-T
*
311462 TTTAAATTTT
1 TTTAAAATTT
311472 TTTAA
1 TTTAA
311477 TAACTTTTGT
Statistics
Matches: 70, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
7 2 0.03
8 6 0.09
9 10 0.14
10 32 0.46
11 20 0.29
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (10 bp):
TTTAAAATTT
Found at i:311440 original size:27 final size:27
Alignment explanation
Indices: 311400--311451 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
311390 AATTTTCCAT
311400 AATTTTTTAAAATA-TATAAATTTTGA
1 AATTTTTTAAAATATTATAAATTTTGA
*
311426 AATTTTTTATAAATATTTTAAATTTT
1 AATTTTTTA-AAATATTATAAATTTT
311452 TAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 5 0.22
28 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
AATTTTTTAAAATATTATAAATTTTGA
Found at i:311450 original size:20 final size:20
Alignment explanation
Indices: 311414--311473 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 20
311404 TTTTAAAATA
*
311414 TATAAAT-TTTGAAATTTTT
1 TATAAATATTTTAAATTTTT
311433 TATAAATATTTTAAA-TTTT
1 TATAAATATTTTAAATTTTT
*
311452 TAAAAATTATTTTAAATTTTT
1 TATAAA-TATTTTAAATTTTT
311473 T
1 T
311474 TAATAACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.44
20 15 0.42
21 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TATAAATATTTTAAATTTTT
Found at i:312102 original size:18 final size:18
Alignment explanation
Indices: 312075--312167 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
312065 TACGACCGTT
*
312075 TACGATACTATTCACGTA
1 TACGGTACTATTCACGTA
*
312093 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
312111 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
312129 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
312147 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
312165 TAC
1 TAC
312168 AGTAGTTGGG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:321820 original size:162 final size:162
Alignment explanation
Indices: 321511--321823 Score: 388
Period size: 162 Copynumber: 1.9 Consensus size: 162
321501 ACCACTTTCT
*
321511 TTTTGGAAGTCAAAACACAACATCACTGAAACCGAGCATTTGTTACAACTGCAACACCTATGGTC
1 TTTTGGAAGTCAAAACACAACATCACTGAAACCGAGCATTTGTTACAAATGCAACACCTATGGTC
*
321576 CCTTTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGAAATGACAATAATAATCAAT
66 CC--TTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGAAATGAAAATAATAATCAAT
** *
321641 GAGTGTATCTTAAAGTGCATTGTTAGAACTTTTA
129 GAACGTATCTCAAAGTGCATTGTTAGAACTTTTA
321675 TTTTGGAAGTCACAACACAACAACATCACTGAAACCTG-GCATTTGTTACAAATGCAA-ATCC-A
1 TTTTGGAAGTCA-AA-AC-ACAACATCACTGAAACC-GAGCATTTGTTACAAATGCAACA-CCTA
* ** * *
321737 CTGGTCCC-T-T-TTTTGGCCAAATCCTTAGTGAATTCTTAGAGCTTTGACGA-GAAAATAATAA
61 -TGGTCCCTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGA-AATGAAAATAATAA
**
321798 TCGGTGAACGTATCTCAAAGTGCATT
124 TCAATGAACGTATCTCAAAGTGCATT
321824 ATTTCTTGAC
Statistics
Matches: 130, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
162 64 0.49
163 2 0.02
164 13 0.10
165 2 0.02
166 4 0.03
167 44 0.34
168 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (162 bp):
TTTTGGAAGTCAAAACACAACATCACTGAAACCGAGCATTTGTTACAAATGCAACACCTATGGTC
CCTTCTCTTTTGACCAAATCCTTAGTGAATTCTTAGAAATTAGAAATGAAAATAATAATCAATGA
ACGTATCTCAAAGTGCATTGTTAGAACTTTTA
Found at i:337700 original size:30 final size:29
Alignment explanation
Indices: 337634--337744 Score: 87
Period size: 31 Copynumber: 3.7 Consensus size: 29
337624 GATTAAATCA
* * * *
337634 AAATTAAAGGTTCAAGTATACATTTGAACC
1 AAATTAAA-GTTCATGTATACAATTGCACT
** * *
337664 ACAATTAGGGTTTCATGTGTATAATTGCACT
1 A-AATTAAAG-TTCATGTATACAATTGCACT
337695 AAATTAAAGTTCATGTATACAATTGCACATT
1 AAATTAAAGTTCATGTATACAATTGCAC--T
**
337726 AAATCGAAGTTCATGTATA
1 AAATTAAAGTTCATGTATA
337745 ATTTTGAGAT
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
29 17 0.27
30 8 0.13
31 38 0.60
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (29 bp):
AAATTAAAGTTCATGTATACAATTGCACT
Found at i:337709 original size:29 final size:30
Alignment explanation
Indices: 337675--337744 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
337665 CAATTAGGGT
* * *
337675 TTCATGTGTATAATTGCAC-TAAATTAAAG
1 TTCATGTATACAATTGCACATAAATCAAAG
*
337704 TTCATGTATACAATTGCACATTAAATCGAAG
1 TTCATGTATACAATTGCACA-TAAATCAAAG
337735 TTCATGTATA
1 TTCATGTATA
337745 ATTTTGAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.49
31 18 0.51
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (30 bp):
TTCATGTATACAATTGCACATAAATCAAAG
Found at i:337792 original size:7 final size:7
Alignment explanation
Indices: 337780--337826 Score: 60
Period size: 7 Copynumber: 6.6 Consensus size: 7
337770 TATATGAAAT
337780 TATTAAA
1 TATTAAA
337787 TATTAAA
1 TATTAAA
337794 TATTAAA
1 TATTAAA
337801 TATTAAAA
1 TATT-AAA
*
337809 TAATATAA
1 TATTA-AA
337817 TA-TAAA
1 TATTAAA
337823 TATT
1 TATT
337827 TAGAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 4 0.11
7 22 0.61
8 10 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TATTAAA
Found at i:350217 original size:55 final size:55
Alignment explanation
Indices: 350133--350244 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
350123 ATGAAAGTTC
*
350133 TGTAAAAGCAACAGGAAAAATTGTTCAGATTTTATTAAATTTTAATAGTTTTCAT
1 TGTAAAAGCAACAGGAAAAATTGTTCAGATTTTATTAAATTTTAAAAGTTTTCAT
350188 TGTAAAAGCAACAGGAAAAATTGTTCAGATTTTATTAAATTTTAAAAGTTTTCAT
1 TGTAAAAGCAACAGGAAAAATTGTTCAGATTTTATTAAATTTTAAAAGTTTTCAT
350243 TG
1 TG
350245 AAGTCACCTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (55 bp):
TGTAAAAGCAACAGGAAAAATTGTTCAGATTTTATTAAATTTTAAAAGTTTTCAT
Found at i:353987 original size:38 final size:38
Alignment explanation
Indices: 353936--354010 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
353926 CCTGAATCCC
353936 GTCATTTGTTGAATAAATAAATACAGTGACAAAATAAG
1 GTCATTTGTTGAATAAATAAATACAGTGACAAAATAAG
*
353974 GTCATTTGTTGAATAAATAAATATAGTGACAAAATAA
1 GTCATTTGTTGAATAAATAAATACAGTGACAAAATAA
354011 AGAGGTCTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.31
Consensus pattern (38 bp):
GTCATTTGTTGAATAAATAAATACAGTGACAAAATAAG
Found at i:354432 original size:4 final size:4
Alignment explanation
Indices: 354423--354465 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
354413 ACACACGTGC
354423 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
354466 ACGACGCACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:360029 original size:16 final size:16
Alignment explanation
Indices: 359992--360046 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
359982 TTAATCATAT
*
359992 TTAAACATA-ATTATAA
1 TTAAA-ATATATTTTAA
360008 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
360023 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
360041 -TAAAAT
1 TTAAAAT
360047 GCTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:360039 original size:18 final size:18
Alignment explanation
Indices: 359998--360046 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
359988 ATATTTAAAC
359998 ATAATTATAATT-AAATAT
1 ATAATT-TAATTAAAATAT
360016 AT--TTTAATTAAAATAT
1 ATAATTTAATTAAAATAT
360032 ATAATTTAA-TAAAAT
1 ATAATTTAATTAAAAT
360047 GCTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 6 0.21
18 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTAATTAAAATAT
Found at i:360165 original size:67 final size:67
Alignment explanation
Indices: 360094--360306 Score: 168
Period size: 67 Copynumber: 3.1 Consensus size: 67
360084 ATTGTTAATG
* *
360094 TTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAATATAAT
1 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAATAAAAT
360159 TA
66 TA
* * * * * * ***
360161 TTATTAAATATATTTTAATTAAAATATATAATT-T-AATAA-AATTCTTATAAT--TAGCAGAAA
1 TTATT---TAAATTTTAA-TAAGAT-TATTATTATCAATAATAAATATTTTAATCATA-TTTAAA
* *
360221 TTACATATTG
60 -TA-AAATTA
* * *
360231 TTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACAAAAT
1 TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAATAAAAT
360296 TA
66 TA
360298 TTA-TTAAAT
1 TTATTTAAAT
360307 ACATTATAAT
Statistics
Matches: 106, Mismatches: 27, Indels: 27
0.66 0.17 0.17
Matches are distributed among these distances:
65 5 0.05
66 12 0.11
67 28 0.26
68 12 0.11
69 14 0.13
70 23 0.22
71 6 0.06
72 6 0.06
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (67 bp):
TTATTTAAATTTTAATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAATAAAAT
TA
Found at i:360167 original size:156 final size:156
Alignment explanation
Indices: 359899--360220 Score: 563
Period size: 156 Copynumber: 2.1 Consensus size: 156
359889 TAGAATACCG
* * *
359899 TTAGCATAAAATTGTTTTAGTAAATGATTATTGTTATTGTTATTTAAATTTTAAAAAGATTATTA
1 TTAGCAGAAAATTATTTTAGTAAATGATTATTGTTAATGTTATTTAAATTTTAAAAAGATTATTA
359964 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
360029 TATATAATTTAATAAAATGCTTATAA
131 TATATAATTTAATAAAATGCTTATAA
* * *
360055 TTAGCAGAAAATTATTTTGGTAGATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAAATTATTTTAGTAAATGATTATTGTTAATGTTATTTAAATTTTAAAAAGATTATTA
* *
360120 TTATCAGTAATAAATATTTTAATCATATTTAAATATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
*
360185 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATGCTTATAA
360211 TTAGCAGAAA
1 TTAGCAGAAA
360221 TTACATATTG
Statistics
Matches: 157, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 157 1.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (156 bp):
TTAGCAGAAAATTATTTTAGTAAATGATTATTGTTAATGTTATTTAAATTTTAAAAAGATTATTA
TTATCAGTAATAAATATTTTAATCATATTTAAACATAATTATAATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATGCTTATAA
Found at i:360190 original size:18 final size:17
Alignment explanation
Indices: 360168--360202 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
360158 TTATTATTAA
*
360168 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
360186 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
360203 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:360238 original size:137 final size:138
Alignment explanation
Indices: 360092--360350 Score: 412
Period size: 137 Copynumber: 1.9 Consensus size: 138
360082 TTATTGTTAA
* * * * *
360092 TGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAATATA
1 TGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACAAA
* *
360157 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT-ATAATTAGCAGAAA
66 ATTATTATTAAATACATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAA
360221 TTACATAT
131 TTACATAT
360229 TGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACAAA
1 TGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACAAA
****
360294 ATTATTATTAAATACATTATAATTTTGGTATATAATTTAATAAAATTCTTAATAATT
66 ATTATTATTAAATACATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
360351 CATATTCTTA
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
137 104 0.95
138 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (138 bp):
TGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACAAA
ATTATTATTAAATACATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAA
TTACATAT
Found at i:360384 original size:137 final size:136
Alignment explanation
Indices: 360106--360384 Score: 328
Period size: 137 Copynumber: 2.0 Consensus size: 136
360096 ATTTAAATTT
* * * * *
360106 TAATAAGATTATTATTATCAGTAATAAATATTTTAATCATATTTAAATATAATTATTATTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACAAAATTATTATTAAATA
* * * *
360171 TATTTTAATTAAAATATATAATTTAATAAAATTCTTATAATTAGCAGAAATTACATATTGTTATT
66 CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTA-CAGAAATTACATAATGTTACT
* **
360236 TAAATTT
130 CAAATCA
360243 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACAAAATTATTATTAAATA
1 TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACAAAATTATTATTAAATA
**** * ** *
360308 CATTATAATTTTGGTATATAATTTAATAAAATTCTTAATAATT-CATATTCTTATATGAAT-TTA
66 CATTATAATTAAAATATATAATTTAATAAAATTCTT-ATAATTACAGA-AATTACAT-AATGTTA
360371 CTCAAATCA
128 CTCAAATCA
360380 TAATA
1 TAATA
360385 TATGATACTA
Statistics
Matches: 119, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
136 3 0.03
137 108 0.91
138 8 0.07
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (136 bp):
TAATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACAAAATTATTATTAAATA
CATTATAATTAAAATATATAATTTAATAAAATTCTTATAATTACAGAAATTACATAATGTTACTC
AAATCA
Found at i:363584 original size:33 final size:33
Alignment explanation
Indices: 363545--363654 Score: 125
Period size: 33 Copynumber: 3.3 Consensus size: 33
363535 ATTATAAAGC
*
363545 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
* *
363578 ATGTATAATTGACCTAAAATTACTTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
* ***
363611 AATGT-T-ATTGTCCCTAAAAAGCATTGTTGGTAT
1 -ATGTATAATTG-ACCTAAAATTAATTGTTGGTAT
363644 ATGTATAATTG
1 ATGTATAATTG
363655 TTGGTTTAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
32 8 0.12
33 49 0.75
34 8 0.12
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:363661 original size:51 final size:51
Alignment explanation
Indices: 363601--363703 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
363591 CTAAAATTAC
*
363601 TTGTTGGTTTAATGTTATTGT-CCCTAAAAAGCATTGTTGGTATATGTATAA
1 TTGTTGGTTTAATGTTATT-TACCCTAAAAAACATTGTTGGTATATGTATAA
*
363652 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTATATGTATAA
363703 T
1 T
363704 CTTTTAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 1 0.02
51 48 0.98
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (51 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTATATGTATAA
Found at i:363880 original size:85 final size:85
Alignment explanation
Indices: 363778--363956 Score: 333
Period size: 85 Copynumber: 2.1 Consensus size: 85
363768 TTCTCTCCAC
363778 ATAA-AATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
363842 TTAATATTAAAGATAAAATT
66 TTAATATTAAAGATAAAATT
*
363862 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCTTGTTTATTATTAATTTCAAATTA
1 ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
363927 TTAATATTAAAGATAAAATT
66 TTAATATTAAAGATAAAATT
*
363947 ATATTAATTA
1 ATAATAATTA
363957 CAATTATATT
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 4 0.04
85 88 0.96
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (85 bp):
ATAATAATTATATCAACATTAATACTTAACAAACAGGTTTCATGTTTATTATTAATTTCAAATTA
TTAATATTAAAGATAAAATT
Found at i:366706 original size:16 final size:16
Alignment explanation
Indices: 366685--366720 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
366675 TTTGGTTCGC
366685 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
366701 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
366717 TGTA
1 TGTA
366721 ATAGAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:366730 original size:16 final size:16
Alignment explanation
Indices: 366695--366740 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
366685 TGTATTGGAT
* * *
366695 TAGAGGTGTATTGGAT
1 TAGAGGTGTAATAGAA
366711 TAGAGGTGTAATAGAA
1 TAGAGGTGTAATAGAA
*
366727 TAGATGTGTAATAG
1 TAGAGGTGTAATAG
366741 CAAATCAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (16 bp):
TAGAGGTGTAATAGAA
Found at i:366783 original size:45 final size:44
Alignment explanation
Indices: 366717--366814 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 44
366707 GGATTAGAGG
* *
366717 TGTAATAGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATAGAATAGATGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* * **
366762 TGTAATGGAATAGA-GACGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATAGAATAGATG-CGTAATAGCAAAACACTGTTTGGTTGAA
366806 TGTAATAGA
1 TGTAATAGA
366815 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 21 0.47
45 24 0.53
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (44 bp):
TGTAATAGAATAGATGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:366994 original size:18 final size:17
Alignment explanation
Indices: 366973--367007 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
366963 TTATTATTTA
*
366973 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
366991 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
367008 TTTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:367140 original size:18 final size:17
Alignment explanation
Indices: 367119--367153 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
367109 TTATTATTAA
*
367119 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
367137 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
367154 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Done.