Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 72 of 93
Found at i:27890315 original size:2 final size:2
Alignment explanation
Indices: 27890310--27890348 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
27890300 TCTCTCTCTT
27890310 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
27890349 GGTAACTTTN
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27890376 original size:2 final size:2
Alignment explanation
Indices: 27890369--27890401 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
27890359 TCTTCTCTTT
27890369 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27890402 AGTGTATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:27890390 original size:15 final size:15
Alignment explanation
Indices: 27890370--27890399 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27890360 CTTCTCTTTT
27890370 ATATATATATATATA
1 ATATATATATATATA
27890385 ATATATATATATATA
1 ATATATATATATATA
27890400 TAAGTGTATA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:27890391 original size:17 final size:17
Alignment explanation
Indices: 27890369--27890402 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27890359 TCTTCTCTTT
27890369 TATATATATATATATAA
1 TATATATATATATATAA
27890386 TATATATATATATATAA
1 TATATATATATATATAA
27890403 GTGTATAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:27894812 original size:35 final size:34
Alignment explanation
Indices: 27894772--27894880 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 34
27894762 ATTGATCTCG
*
27894772 TGAAAAGCCATTGTTGTAGGTTGTGGTTGAGCCTT
1 TGAAAAACCATTGTTG-AGGTTGTGGTTGAGCCTT
** **
27894807 TGAAAAACCA-CATTG-GGCTT-TGGTTGAGCCCG
1 TGAAAAACCATTGTTGAGG-TTGTGGTTGAGCCTT
27894839 TGAAAAACCATTG-TGAAAGGTTGTGGTTGAGCCTT
1 TGAAAAACCATTGTTG--AGGTTGTGGTTGAGCCTT
27894874 TGAAAAA
1 TGAAAAA
27894881 TCACTTTGGG
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
32 24 0.41
33 2 0.03
34 5 0.08
35 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (34 bp):
TGAAAAACCATTGTTGAGGTTGTGGTTGAGCCTT
Found at i:27894832 original size:32 final size:31
Alignment explanation
Indices: 27894795--27894900 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 31
27894785 TTGTAGGTTG
27894795 TGGTTGAGCCTTTGAAAAACCACATTGGGCTT
1 TGGTTGAGCCTTTGAAAAA-CACATTGGGCTT
** *
27894827 TGGTTGAGCCCGTGAAAAAC-CATTGTGAAAGGTT
1 TGGTTGAGCCTTTGAAAAACACATTG-G---GCTT
* *
27894861 GTGGTTGAGCCTTTGAAAAATCACTTTGGGTTT
1 -TGGTTGAGCCTTTGAAAAA-CACATTGGGCTT
27894894 TGGTTGA
1 TGGTTGA
27894901 TCGTGGTAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
30 5 0.08
31 2 0.03
32 24 0.40
33 3 0.05
34 3 0.05
35 17 0.28
36 2 0.03
37 4 0.07
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (31 bp):
TGGTTGAGCCTTTGAAAAACACATTGGGCTT
Found at i:27894842 original size:67 final size:67
Alignment explanation
Indices: 27894752--27894923 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
27894742 AAGTTAGTTG
* * * * *
27894752 TTGGGTTTTGATTGATCTCGTGAAAAGCCATTGTTG-TAGGTTGTGGTTGAGCCTTTGAAAAACC
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTG-TGAAAGGTTGTGGTTGAGCCTTTGAAAAACC
27894816 ACA
65 ACA
* *
27894819 TTGGGCTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCA
1 TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
*
27894884 CT
66 CA
*
27894886 TTGGGTTTTGGTTGA--TCGTGGTAAAAACCATTGTGAAA
1 TTGGGTTTTGGTTGAGCCCGT-G-AAAAACCATTGTGAAA
27894924 AGTTTTGGCT
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
65 3 0.03
66 3 0.03
67 86 0.93
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (67 bp):
TTGGGTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
CA
Found at i:27894939 original size:67 final size:66
Alignment explanation
Indices: 27894791--27894939 Score: 174
Period size: 67 Copynumber: 2.2 Consensus size: 66
27894781 ATTGTTGTAG
* *
27894791 GTTGTGGTTGAGCCTTTGAAAAACCACATTGGGCTTTGGTTGAGCCCGTGAAAAACCATTGTGAA
1 GTTGTGGCTAAGCCTTTGAAAAACCACATTGGGCTTTGGTTGA-CCCGTGAAAAACCATTGTGAA
*
27894856 AG
65 AA
* * * * * *
27894858 GTTGTGGTTGAGCCTTTGAAAAATCACTTTGGGTTTTGGTTGA-TCGTGGTAAAAACCATTGTGA
1 GTTGTGGCTAAGCCTTTGAAAAACCACATTGGGCTTTGGTTGACCCGT-G-AAAAACCATTGTGA
27894922 AAA
64 AAA
*
27894925 GTTTTGGCTAAGCCT
1 GTTGTGGCTAAGCCT
27894940 GGTAAAAGCC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
65 3 0.04
66 1 0.01
67 68 0.94
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (66 bp):
GTTGTGGCTAAGCCTTTGAAAAACCACATTGGGCTTTGGTTGACCCGTGAAAAACCATTGTGAAA
A
Found at i:27895897 original size:15 final size:15
Alignment explanation
Indices: 27895879--27895909 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27895869 ATTTAGTTAA
*
27895879 ATTTTATGTTATTTT
1 ATTTTATATTATTTT
27895894 ATTTTATATTATTTT
1 ATTTTATATTATTTT
27895909 A
1 A
27895910 AAAGTAGTTA
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:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTATATTATTTT
Found at i:27897268 original size:17 final size:16
Alignment explanation
Indices: 27897246--27897298 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
27897236 TTCTCAACTT
27897246 ATTTAGTTTTTTAGTTA
1 ATTTAGTTTTTT-GTTA
27897263 ATTTAGTATTTATT-TTA
1 ATTTAGT-TTT-TTGTTA
*
27897280 ATTTTG-TTTTTGTTA
1 ATTTAGTTTTTTGTTA
27897295 ATTT
1 ATTT
27897299 TCTACAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 2 0.06
15 10 0.31
17 15 0.47
18 3 0.09
19 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (16 bp):
ATTTAGTTTTTTGTTA
Found at i:27901811 original size:40 final size:40
Alignment explanation
Indices: 27901753--27901833 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
27901743 GGAAGCCATT
* *
27901753 ACCACTAGACCACAGCACCACGACACCGCCAAACCACCAA
1 ACCACCAGACCACAGCACCACGACACCACCAAACCACCAA
* * * *
27901793 ACCACCAGACCACGGCACCATGGCACCACCAGACCACCAA
1 ACCACCAGACCACAGCACCACGACACCACCAAACCACCAA
27901833 A
1 A
27901834 TCTTTCTTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.47, G:0.12, T:0.02
Consensus pattern (40 bp):
ACCACCAGACCACAGCACCACGACACCACCAAACCACCAA
Found at i:27912845 original size:13 final size:13
Alignment explanation
Indices: 27912827--27912852 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27912817 GGAGCCATAT
27912827 ACTCCATTACAAG
1 ACTCCATTACAAG
27912840 ACTCCATTACAAG
1 ACTCCATTACAAG
27912853 GCTTAGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
ACTCCATTACAAG
Found at i:27920649 original size:41 final size:42
Alignment explanation
Indices: 27920553--27920642 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
27920543 TTAATATTTT
* * *
27920553 AATTATACATAAAATATTAATATTTTAAAATGTTAATGATTA
1 AATTATAAATAAAATATTAATATTTTAAAATATCAATGATTA
* *
27920595 AATTATAAATAAAATATTAATA-TTTAAATTATCAATTATTA
1 AATTATAAATAAAATATTAATATTTTAAAATATCAATGATTA
27920636 ATATTAT
1 A-ATTAT
27920643 TATAAAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 16 0.38
42 26 0.62
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (42 bp):
AATTATAAATAAAATATTAATATTTTAAAATATCAATGATTA
Found at i:27927311 original size:2 final size:2
Alignment explanation
Indices: 27927304--27927328 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27927294 TAATAATTAC
27927304 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
27927329 GATAAGCAAC
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:27937836 original size:19 final size:18
Alignment explanation
Indices: 27937797--27937838 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
27937787 TTTTAGTTAT
*
27937797 TTTTA-TAATTAGTTTAT
1 TTTTATTAATTAGTTTAA
*
27937814 TTTTATTAAGTTATTTTAA
1 TTTTATTAA-TTAGTTTAA
27937833 TTTTAT
1 TTTTAT
27937839 GTTTATTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 3 0.14
19 13 0.62
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTATTAATTAGTTTAA
Found at i:27941361 original size:28 final size:28
Alignment explanation
Indices: 27941324--27941397 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
27941314 TGGGTGGTGT
* *
27941324 AAAATTACAATTTTGCCCATAGGGTGGC
1 AAAATGACAATTTTGCCCATAGGGTGAC
*
27941352 AAAATGACAATTTTGCCCCTAGGGTGAC
1 AAAATGACAATTTTGCCCATAGGGTGAC
*
27941380 AAAATGACTATTTTGCCC
1 AAAATGACAATTTTGCCC
27941398 TTATGCTCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (28 bp):
AAAATGACAATTTTGCCCATAGGGTGAC
Found at i:27941411 original size:28 final size:28
Alignment explanation
Indices: 27941324--27941411 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 28
27941314 TGGGTGGTGT
* * * **
27941324 AAAATTACAATTTTGCCCATAGGGTGGC
1 AAAATGACAATTTTGCCCCTAGGCTCAC
* *
27941352 AAAATGACAATTTTGCCCCTAGGGTGAC
1 AAAATGACAATTTTGCCCCTAGGCTCAC
* * * *
27941380 AAAATGACTATTTTGCCCTTATGCTCAG
1 AAAATGACAATTTTGCCCCTAGGCTCAC
27941408 AAAA
1 AAAA
27941412 ATGCTGGAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (28 bp):
AAAATGACAATTTTGCCCCTAGGCTCAC
Found at i:27955602 original size:5 final size:5
Alignment explanation
Indices: 27955570--27955615 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
27955560 TATTTTTTCA
*
27955570 TTTAT TATTAT TTAAT TATTATT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT T-TTAT TTTAT T-TTA-T TTTAT TTTAT TTTAT TTTAT TTT
27955616 TTTATTATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 24 0.67
6 10 0.28
7 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:27955616 original size:11 final size:11
Alignment explanation
Indices: 27955570--27955623 Score: 67
Period size: 10 Copynumber: 5.0 Consensus size: 11
27955560 TATTTTTTCA
27955570 TTTATTATTAT
1 TTTATTATTAT
*
27955581 TTAATTATTATT
1 TTTATTATTA-T
27955593 TTTATT-TTAT
1 TTTATTATTAT
27955603 TTTATT-TTAT
1 TTTATTATTAT
*
27955613 TTTTTTATTAT
1 TTTATTATTAT
27955624 CATATTTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 16 0.42
11 16 0.42
12 6 0.16
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:27955623 original size:16 final size:16
Alignment explanation
Indices: 27955560--27955637 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
27955550 TGCAATTATC
*
27955560 TATTTTTTCATTTATTAT
1 TATTTTTTTA-TTATT-T
**
27955578 TATTTAATTATTATTTT
1 TATTTTTTTATTA-TTT
*
27955595 TATTTTATT-TTATTT
1 TATTTTTTTATTATTT
**
27955610 TATTTTTTTATTATCA
1 TATTTTTTTATTATTT
*
27955626 TATTTTTCTATT
1 TATTTTTTTATT
27955638 TTATTTCTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
15 11 0.22
16 18 0.36
17 12 0.24
18 9 0.18
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTTTTATTATTT
Found at i:27955629 original size:21 final size:20
Alignment explanation
Indices: 27955554--27955660 Score: 60
Period size: 21 Copynumber: 5.0 Consensus size: 20
27955544 TGCTAATGCA
27955554 ATTATCTATTTT-TTCATTTATT
1 ATTATCTATTTTATT--TTT-TT
*
27955576 ATTATTTAATTATTATTTTTATT
1 ATTATCT-ATT-TTATTTTT-TT
*
27955599 -TTATTTTATTTTATTTTTTT
1 ATTA-TCTATTTTATTTTTTT
*
27955619 ATTATCATATTTT-TCTATTTT
1 ATTATC-TATTTTAT-TTTTTT
27955640 ATT-TCTAATTATTATTTTTTT
1 ATTATCT-ATT-TTATTTTTTT
27955661 CATACTTTAC
Statistics
Matches: 71, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
19 1 0.01
20 9 0.13
21 32 0.45
22 13 0.18
23 12 0.17
24 2 0.03
25 2 0.03
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTATCTATTTTATTTTTTT
Found at i:27955654 original size:13 final size:12
Alignment explanation
Indices: 27955572--27955656 Score: 57
Period size: 11 Copynumber: 7.9 Consensus size: 12
27955562 TTTTTTCATT
27955572 TATTATTATTT-
1 TATTATTATTTC
* *
27955583 AATTATTATTTT
1 TATTATTATTTC
27955595 TATT-TTATTT-
1 TATTATTATTTC
27955605 TATT-TTATTT-
1 TATTATTATTTC
*
27955615 TTTTATTA--TC
1 TATTATTATTTC
27955625 -A-TATT-TTTC
1 TATTATTATTTC
27955634 TATT-TTATTTC
1 TATTATTATTTC
27955645 TAATTATTATTT
1 T-ATTATTATTT
27955657 TTTTCATACT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
10 16 0.27
11 25 0.42
12 6 0.10
13 6 0.10
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTATTATTTC
Found at i:27955933 original size:14 final size:13
Alignment explanation
Indices: 27955891--27955948 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 13
27955881 ATTCGAATTA
27955891 TTAT-TATTATTT
1 TTATCTATTATTT
27955903 TTATCATCATT-TTT
1 TTATC-T-ATTATTT
*
27955917 TTATCTATTGTTAT
1 TTATCTATTATT-T
*
27955931 TTATTTATTATTT
1 TTATCTATTATTT
27955944 TTATC
1 TTATC
27955949 GAGTAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 7 0.18
13 8 0.21
14 20 0.53
15 3 0.08
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (13 bp):
TTATCTATTATTT
Found at i:27956201 original size:11 final size:11
Alignment explanation
Indices: 27956185--27956234 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
27956175 TACATAAAGC
27956185 TATATTATTAT
1 TATATTATTAT
27956196 TATATTATT-T
1 TATATTATTAT
* *
27956206 TTTATTTACTAT
1 TATA-TTATTAT
*
27956218 T-TATTATTTT
1 TATATTATTAT
27956228 TATATTA
1 TATATTA
27956235 AATGTTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 10 0.31
11 20 0.62
12 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTATTAT
Found at i:27956212 original size:7 final size:7
Alignment explanation
Indices: 27956189--27956230 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
27956179 TAAAGCTATA
27956189 TTATTAT
1 TTATTAT
27956196 TATATTAT
1 T-TATTAT
*
27956204 TTTTTAT
1 TTATTAT
*
27956211 TTACTAT
1 TTATTAT
27956218 TTATTAT
1 TTATTAT
27956225 TT-TTAT
1 TTATTAT
27956231 ATTAAATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTAT
Found at i:27956730 original size:16 final size:16
Alignment explanation
Indices: 27956711--27956741 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27956701 TTTTTTTTTC
*
27956711 TTTTCTTTTCTTCTTT
1 TTTTCTTTCCTTCTTT
27956727 TTTTCTTTCCTTCTT
1 TTTTCTTTCCTTCTT
27956742 CCACCGTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTCCTTCTTT
Found at i:27957720 original size:1 final size:1
Alignment explanation
Indices: 27957716--27957790 Score: 60
Period size: 1 Copynumber: 75.0 Consensus size: 1
27957706 TGGTTAGTTA
* * * * * * * * * *
27957716 TTTTTTTTGTTTTTCTATTTTTGTTTTTTTTTTGTTTTTGTTTTTGTTTTTTTGTTTTTCTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27957781 TTTTTTTTTT
1 TTTTTTTTTT
27957791 AAATTTTGCA
Statistics
Matches: 54, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:27957736 original size:14 final size:14
Alignment explanation
Indices: 27957719--27957787 Score: 68
Period size: 14 Copynumber: 4.8 Consensus size: 14
27957709 TTAGTTATTT
*
27957719 TTTTTGTTTTTCTA
1 TTTTTGTTTTTCTG
*
27957733 TTTTTGTTTTTTTTTTG
1 TTTTTG---TTTTTCTG
* *
27957750 TTTTTGTTTTTGTT
1 TTTTTGTTTTTCTG
27957764 TTTTTGTTTTTCTG
1 TTTTTGTTTTTCTG
27957778 TTTTT-TTTTT
1 TTTTTGTTTTT
27957788 TTTAAATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.11
14 29 0.63
17 12 0.26
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTTTCTG
Found at i:27957744 original size:8 final size:8
Alignment explanation
Indices: 27957733--27957790 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
27957723 TGTTTTTCTA
27957733 TTTTTGTT
1 TTTTTGTT
27957741 TTTTT-TT
1 TTTTTGTT
*
27957748 TGTTTT-TG
1 T-TTTTGTT
27957756 TTTTTGTT
1 TTTTTGTT
27957764 TTTTTGTT
1 TTTTTGTT
*
27957772 TTTCTGTT
1 TTTTTGTT
27957780 TTTTT-TT
1 TTTTTGTT
27957787 TTTT
1 TTTT
27957791 AAATTTTGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
7 13 0.30
8 31 0.70
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (8 bp):
TTTTTGTT
Found at i:27957798 original size:37 final size:37
Alignment explanation
Indices: 27957720--27957798 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
27957710 TAGTTATTTT
* ***
27957720 TTTTGTTTTTCTATTTTTGTTTTTTTTTTGTTTTTGT
1 TTTTGTTTTTCTATTTTTCTTTTTTTTTTGTTTTAAA
* *
27957757 TTTTGTTTTTTTGTTTTTCTGTTTTTTTTT-TTTTAAA
1 TTTTGTTTTTCTATTTTTCT-TTTTTTTTTGTTTTAAA
27957794 TTTTG
1 TTTTG
27957799 CAGCCTTGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 26 0.74
38 9 0.26
ACGTcount: A:0.05, C:0.03, G:0.10, T:0.82
Consensus pattern (37 bp):
TTTTGTTTTTCTATTTTTCTTTTTTTTTTGTTTTAAA
Found at i:27977439 original size:19 final size:19
Alignment explanation
Indices: 27977415--27977452 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
27977405 CTGCCAAACC
*
27977415 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
27977434 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
27977453 AGTCAAATGG
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:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:27980451 original size:27 final size:26
Alignment explanation
Indices: 27980409--27980513 Score: 86
Period size: 29 Copynumber: 3.7 Consensus size: 26
27980399 AATGCAATTA
*
27980409 TCTA-TTTATTTATTTATTATTTTTAT
1 TCTATTTTATTTTTTTATTATTTTT-T
*
27980435 TTTATTTTATTTTTTTATTATCATATTTT
1 TCTATTTTATTTTTTTATTAT--T-TTTT
*
27980464 TCTATTTTATTTCTAATTATTATTTTTT
1 TCTATTTTATTT-T-TTTATTATTTTTT
*
27980492 TCATACTTTACATTTTTTTATT
1 TC-TA-TTT-TATTTTTTTATT
27980514 CTAAGTTTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
26 3 0.05
27 15 0.23
28 6 0.09
29 21 0.33
30 8 0.12
31 11 0.17
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (26 bp):
TCTATTTTATTTTTTTATTATTTTTT
Found at i:27980474 original size:13 final size:12
Alignment explanation
Indices: 27980413--27980491 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 12
27980403 CAATTATCTA
27980413 TTTA-TTTATTT
1 TTTATTTTATTT
* *
27980424 ATTATTTT-TAT
1 TTTATTTTATTT
27980435 TTTATTTTATTTT
1 TTTATTTTA-TTT
27980448 TTTATTATCATATTT
1 TTTATT-T--TATTT
27980463 TTCTATTTTATTT
1 TT-TATTTTATTT
* *
27980476 CTAATTATTATTT
1 TTTATT-TTATTT
27980489 TTT
1 TTT
27980492 TCATACTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
11 12 0.23
12 6 0.12
13 21 0.40
14 1 0.02
15 6 0.12
16 6 0.12
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:27980622 original size:16 final size:14
Alignment explanation
Indices: 27980601--27980663 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 14
27980591 TTATTATTAT
27980601 TTTTATCATTTTTGTA
1 TTTTAT-ATTTTT-TA
27980617 TTTTATATTTTTTA
1 TTTTATATTTTTTA
27980631 TTATTATTATTTATTT-
1 TT-TTA-TATTT-TTTA
27980647 TTTTA-ATTTTTCTA
1 TTTTATATTTTT-TA
27980661 TTT
1 TTT
27980664 ATTTGATGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.05
13 5 0.12
14 7 0.17
15 12 0.29
16 13 0.31
17 3 0.07
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTATATTTTTTA
Found at i:27980650 original size:21 final size:21
Alignment explanation
Indices: 27980597--27980667 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
27980587 AAATTTATTA
* * *
27980597 TTATTTTTATCATTTTTGTATT
1 TTATTTTTTTAATTTTTCTA-T
27980619 TTATATTTTTT-ATTATTAT-TAT
1 TTAT-TTTTTTAATT-TT-TCTAT
27980641 TTATTTTTTTAATTTTTCTAT
1 TTATTTTTTTAATTTTTCTAT
27980662 TTATTT
1 TTATTT
27980668 GATGTCATGT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
20 1 0.02
21 17 0.40
22 15 0.35
23 9 0.21
24 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (21 bp):
TTATTTTTTTAATTTTTCTAT
Found at i:27981033 original size:8 final size:8
Alignment explanation
Indices: 27981017--27981070 Score: 65
Period size: 8 Copynumber: 6.4 Consensus size: 8
27981007 TATAAAGCTA
27981017 TATTATTAT
1 TATT-TTAT
27981026 TATTTTAT
1 TATTTTAT
27981034 T-TTTTAT
1 TATTTTAT
27981041 TAACTATTTAT
1 T-A-T-TTTAT
27981052 TATTTTAT
1 TATTTTAT
27981060 TATTTTAT
1 TATTTTAT
27981068 TAT
1 TAT
27981071 GTTAAATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.17
8 21 0.51
9 5 0.12
10 2 0.05
11 6 0.15
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (8 bp):
TATTTTAT
Found at i:27981557 original size:10 final size:10
Alignment explanation
Indices: 27981539--27981572 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
27981529 AGCTGCCCCT
27981539 TTTTTTTTTC
1 TTTTTTTTTC
*
27981549 TTTTCTTTTC
1 TTTTTTTTTC
27981559 TTTTTTTCTTC
1 TTTTTTT-TTC
27981570 TTT
1 TTT
27981573 CCTTCTTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:28009673 original size:23 final size:23
Alignment explanation
Indices: 28009630--28009673 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28009620 TGTTGCAAGG
*
28009630 TTACCATGTGGCATGCCAAGAGA
1 TTACCATGTGGCATACCAAGAGA
* *
28009653 TTACCATGTGGGATACTAAGA
1 TTACCATGTGGCATACCAAGA
28009674 TTCTACCACG
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:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (23 bp):
TTACCATGTGGCATACCAAGAGA
Found at i:28011789 original size:48 final size:49
Alignment explanation
Indices: 28011736--28011828 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
28011726 TATTATTTTT
28011736 TTTACTCGCACACCAAGTAAG-TTAGGTTTAGTTAGCTATTATAATTAC
1 TTTACTCGCACACCAAGTAAGTTTAGGTTTAGTTAGCTATTATAATTAC
* *
28011784 TTTACTTGCACATCAAGTAAGTTTAGGTTTAGTTAGCTATTATAA
1 TTTACTCGCACACCAAGTAAGTTTAGGTTTAGTTAGCTATTATAA
28011829 ATAGCTTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
48 19 0.45
49 23 0.55
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (49 bp):
TTTACTCGCACACCAAGTAAGTTTAGGTTTAGTTAGCTATTATAATTAC
Found at i:28014649 original size:27 final size:27
Alignment explanation
Indices: 28014619--28014672 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
28014609 TCTCCCTCAA
* *
28014619 ATAATCTTGAATCCCATATCTGATGAG
1 ATAATCCTAAATCCCATATCTGATGAG
*
28014646 ATAATCCTAAATCCCATATTTGATGAG
1 ATAATCCTAAATCCCATATCTGATGAG
28014673 TCCCATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (27 bp):
ATAATCCTAAATCCCATATCTGATGAG
Found at i:28019986 original size:73 final size:72
Alignment explanation
Indices: 28019865--28020020 Score: 242
Period size: 73 Copynumber: 2.2 Consensus size: 72
28019855 AGAATTATGT
* * * *
28019865 TTGGGAATGAATGTTTAGAATTATTGTTTAGATTTTTAATTAAAATGATTGGTAATATTCTAGAA
1 TTGGGAATTAATGTTGAGAATTATTCTTTAGATTTTTAATTAAAATGATTGGTAATATGCTAGAA
*
28019930 TTAAATA
66 TTAAACA
*
28019937 TTGGGGAATTAATGTTGAGAATTATTCTTTGGATTTTTAATTAAAATGATTGGTAATATGCTAGA
1 TT-GGGAATTAATGTTGAGAATTATTCTTTAGATTTTTAATTAAAATGATTGGTAATATGCTAGA
28020002 ATTAAACA
65 ATTAAACA
28020010 TT-GGAATTAAT
1 TTGGGAATTAAT
28020021 ATTTGGGTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
71 9 0.12
72 2 0.03
73 66 0.86
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.43
Consensus pattern (72 bp):
TTGGGAATTAATGTTGAGAATTATTCTTTAGATTTTTAATTAAAATGATTGGTAATATGCTAGAA
TTAAACA
Found at i:28022662 original size:25 final size:25
Alignment explanation
Indices: 28022630--28022683 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
28022620 CTTTTGAAAC
*
28022630 TAATGTTTATTTATTATATAAAGAT
1 TAATGTTTATTTATTACATAAAGAT
* *
28022655 TAATGTTTATTTATTGCATGAAGAT
1 TAATGTTTATTTATTACATAAAGAT
28022680 TAAT
1 TAAT
28022684 ATTATTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (25 bp):
TAATGTTTATTTATTACATAAAGAT
Found at i:28026702 original size:11 final size:10
Alignment explanation
Indices: 28026686--28026749 Score: 56
Period size: 11 Copynumber: 6.1 Consensus size: 10
28026676 AAAGGGATGT
28026686 TCAAATTTAAA
1 TCAAATTT-AA
*
28026697 TCAAATCCTAA
1 TCAAAT-TTAA
**
28026708 TCAAATCAAA
1 TCAAATTTAA
28026718 TCAAATTCTAA
1 TCAAATT-TAA
* *
28026729 GCAAATTTAT
1 TCAAATTTAA
28026739 TCAAATTTAA
1 TCAAATTTAA
28026749 T
1 T
28026750 TACATAAGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
10 20 0.47
11 22 0.51
12 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (10 bp):
TCAAATTTAA
Found at i:28026720 original size:21 final size:21
Alignment explanation
Indices: 28026694--28026734 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28026684 GTTCAAATTT
*
28026694 AAATCAAATCCTAATCAAATC
1 AAATCAAATCCTAAGCAAATC
*
28026715 AAATCAAATTCTAAGCAAAT
1 AAATCAAATCCTAAGCAAAT
28026735 TTATTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.24
Consensus pattern (21 bp):
AAATCAAATCCTAAGCAAATC
Found at i:28034051 original size:28 final size:28
Alignment explanation
Indices: 28034020--28034219 Score: 151
Period size: 27 Copynumber: 7.3 Consensus size: 28
28034010 GTTTAACGAT
* *
28034020 TAAATTTTTCAATATGATATATAACAAC
1 TAAATTTTTCAATATGACATGTAACAAC
* * *
28034048 TAAA-TCTTCAACATGACGTGTAACAAC
1 TAAATTTTTCAATATGACATGTAACAAC
* * *
28034075 TAAAATTTT-AACATGGCATGTAACAAC
1 TAAATTTTTCAATATGACATGTAACAAC
* * *
28034102 TACATTTTTCAATATAACATGTAATAAC
1 TAAATTTTTCAATATGACATGTAACAAC
**
28034130 TAAA-TTTTCAATAT-AGTGTGTAACAAC
1 TAAATTTTTCAATATGA-CATGTAACAAC
* * *
28034157 TAAATTTTTTAATAT-AGTATATAACAAC
1 TAAATTTTTCAATATGA-CATGTAACAAC
* * * *
28034185 TAAA-TTTTCAACATAACGTGTAACAAT
1 TAAATTTTTCAATATGACATGTAACAAC
*
28034212 TACATTTT
1 TAAATTTT
28034220 CAACGTGATT
Statistics
Matches: 138, Mismatches: 28, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
26 1 0.01
27 85 0.62
28 52 0.38
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (28 bp):
TAAATTTTTCAATATGACATGTAACAAC
Found at i:28034113 original size:55 final size:55
Alignment explanation
Indices: 28033996--28034165 Score: 155
Period size: 55 Copynumber: 3.1 Consensus size: 55
28033986 GTGTAACAAC
* * * * * * *
28033996 TTTTTCATCATGACGTTTAACGATTAAATTTTTCAATATGATATATAACAACTAA
1 TTTTTCAACATGACGTGTAACAACTAAAATTTTCAATATGGTATGTAACAACTAA
* * * *
28034051 ATCTTCAACATGACGTGTAACAACTAAAATTTT-AACATGGCATGTAACAACTACA
1 TTTTTCAACATGACGTGTAACAACTAAAATTTTCAATATGGTATGTAACAACTA-A
* * * * * *
28034106 TTTTTCAATATAACATGTAATAACT-AAATTTTCAATATAGTGTGTAACAACTAAA
1 TTTTTCAACATGACGTGTAACAACTAAAATTTTCAATATGGTATGTAACAACT-AA
28034161 TTTTT
1 TTTTT
28034166 TAATATAGTA
Statistics
Matches: 91, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
54 23 0.25
55 67 0.74
56 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (55 bp):
TTTTTCAACATGACGTGTAACAACTAAAATTTTCAATATGGTATGTAACAACTAA
Found at i:28034131 original size:82 final size:82
Alignment explanation
Indices: 28034022--28034210 Score: 211
Period size: 82 Copynumber: 2.3 Consensus size: 82
28034012 TTAACGATTA
* * *
28034022 AATTTTTCAATATGATATATAACAACTAAATCTTCAACAT-GACGTGTAACAACTAAA-ATTTTA
1 AATTTTTCAATATAACATGTAACAACTAAATCTTCAACATAG-CGTGTAACAACTAAATATTTTA
* *
28034085 ACATGGCATGTAACAACT
65 ACATAGCATATAACAACT
* * * * *
28034103 ACATTTTTCAATATAACATGTAATAACTAAATTTTCAATATAGTGTGTAACAACTAAATTTTTTA
1 A-ATTTTTCAATATAACATGTAACAACTAAATCTTCAACATAGCGTGTAACAACTAAATATTTTA
* *
28034168 ATATAGTATATAACAACT
65 ACATAGCATATAACAACT
* * *
28034186 AAATTTTCAACATAACGTGTAACAA
1 AATTTTTCAATATAACATGTAACAA
28034211 TTACATTTTC
Statistics
Matches: 89, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
81 1 0.01
82 67 0.75
83 21 0.24
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (82 bp):
AATTTTTCAATATAACATGTAACAACTAAATCTTCAACATAGCGTGTAACAACTAAATATTTTAA
CATAGCATATAACAACT
Found at i:28034171 original size:55 final size:55
Alignment explanation
Indices: 28034068--28034219 Score: 171
Period size: 55 Copynumber: 2.8 Consensus size: 55
28034058 ACATGACGTG
** * *
28034068 TAACAACTAAAATTTT-AACATGGCATGTAACAACTACATTTTTCAATATAACATG
1 TAACAACT-AAATTTTCAACATAACGTGTAACAACTACATTTTTCAATATAACATA
* * ** * * **
28034123 TAATAACTAAATTTTCAATATAGTGTGTAACAACTAAATTTTTTAATATAGTATA
1 TAACAACTAAATTTTCAACATAACGTGTAACAACTACATTTTTCAATATAACATA
*
28034178 TAACAACTAAATTTTCAACATAACGTGTAACAATTACATTTT
1 TAACAACTAAATTTTCAACATAACGTGTAACAACTACATTTT
28034220 CAACGTGATT
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 7 0.09
55 73 0.91
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (55 bp):
TAACAACTAAATTTTCAACATAACGTGTAACAACTACATTTTTCAATATAACATA
Found at i:28042545 original size:2 final size:2
Alignment explanation
Indices: 28042534--28042570 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
28042524 TCTTTAATTT
28042534 TA TA -A TA TA TA TA TA 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 TA TA TA TA
28042571 CACACACTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28044425 original size:23 final size:22
Alignment explanation
Indices: 28044400--28044441 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28044390 ATTTCTGTTT
* *
28044400 TTTTTCTTTTCCTTTTTGTCTC
1 TTTTTGTTTTTCTTTTTGTCTC
28044422 TTTTTGTTTTTCTTTTTGTC
1 TTTTTGTTTTTCTTTTTGTC
28044442 CAAGTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTTGTTTTTCTTTTTGTCTC
Found at i:28044980 original size:14 final size:13
Alignment explanation
Indices: 28044961--28044998 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
28044951 ATTTAGGTAT
28044961 TATTTTGTTCTTTC
1 TATTTTGTT-TTTC
28044975 TATTTTGTTTTTC
1 TATTTTGTTTTTC
*
28044988 -ATTTTCTTTTT
1 TATTTTGTTTTT
28044999 GTCATTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 4 0.17
14 9 0.39
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (13 bp):
TATTTTGTTTTTC
Found at i:28048953 original size:18 final size:18
Alignment explanation
Indices: 28048926--28048965 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28048916 AATTGTTGAT
* *
28048926 TTATGAGTTATTTATGAA
1 TTATGAGTTACTTATAAA
*
28048944 TTATGTGTTACTTATAAA
1 TTATGAGTTACTTATAAA
28048962 TTAT
1 TTAT
28048966 TTGTGGAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (18 bp):
TTATGAGTTACTTATAAA
Found at i:28049340 original size:14 final size:15
Alignment explanation
Indices: 28049321--28049354 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28049311 CCAATTATAT
28049321 ATTAAATAT-ATTGA
1 ATTAAATATAATTGA
*
28049335 ATTAAATATAATTTA
1 ATTAAATATAATTGA
28049350 ATTAA
1 ATTAA
28049355 GAAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
ATTAAATATAATTGA
Found at i:28056664 original size:57 final size:57
Alignment explanation
Indices: 28056574--28056687 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
28056564 TTAGGACATG
*
28056574 TTAGTATGCTCACAATTTCAAAACTTTTTAAAAAAGACTTAGTCATTGGACTTCCAA
1 TTAGTATGCTCACAATTTCAAAACTTTTGAAAAAAGACTTAGTCATTGGACTTCCAA
28056631 TTAGTATGCTCACAATTTCAAAACTTTTGAAAAAAGACTTAGTCATTGGACTTCCAA
1 TTAGTATGCTCACAATTTCAAAACTTTTGAAAAAAGACTTAGTCATTGGACTTCCAA
28056688 ACATATCATT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (57 bp):
TTAGTATGCTCACAATTTCAAAACTTTTGAAAAAAGACTTAGTCATTGGACTTCCAA
Found at i:28076983 original size:15 final size:15
Alignment explanation
Indices: 28076963--28076996 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
28076953 CATACATAAG
28076963 GGAAACTCCAATATA
1 GGAAACTCCAATATA
28076978 GGAAACTCCAATATA
1 GGAAACTCCAATATA
28076993 GGAA
1 GGAA
28076997 GCATAAAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (15 bp):
GGAAACTCCAATATA
Found at i:28077349 original size:13 final size:13
Alignment explanation
Indices: 28077331--28077355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28077321 GTTAATGCTC
28077331 AAGTCTTATTAAT
1 AAGTCTTATTAAT
28077344 AAGTCTTATTAA
1 AAGTCTTATTAA
28077356 GAATGTGAGC
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
AAGTCTTATTAAT
Found at i:28081937 original size:17 final size:18
Alignment explanation
Indices: 28081895--28081928 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28081885 AATGGTTAAG
28081895 AAAAGAA-AACTTAAAAC
1 AAAAGAATAACTTAAAAC
28081912 AAAAGAATAACTTAAAA
1 AAAAGAATAACTTAAAA
28081929 AAATAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAAGAATAACTTAAAAC
Found at i:28085939 original size:2 final size:2
Alignment explanation
Indices: 28085932--28085960 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28085922 CGATCTTCAT
28085932 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
28085961 GTATGACTAT
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:28088458 original size:38 final size:38
Alignment explanation
Indices: 28088407--28088486 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
28088397 ACGGTAAGTT
*
28088407 GATTACAAGGTTAGAAGAGGTCCGTTGCATTGGACAAG
1 GATTACAAGGTTAGAAGAGGTCCGTTACATTGGACAAG
*
28088445 GATTACGAGGTTAGAAGAGGTCCGTTACATTGGACAAG
1 GATTACAAGGTTAGAAGAGGTCCGTTACATTGGACAAG
28088483 GATT
1 GATT
28088487 TGATGATGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.25
Consensus pattern (38 bp):
GATTACAAGGTTAGAAGAGGTCCGTTACATTGGACAAG
Found at i:28106272 original size:15 final size:15
Alignment explanation
Indices: 28106252--28106289 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
28106242 AAATAGACAT
*
28106252 ATAATAGTAACAATA
1 ATAATAATAACAATA
28106267 ATAATAATAACAATA
1 ATAATAATAACAATA
28106282 ATAATAAT
1 ATAATAAT
28106290 CTAGTTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (15 bp):
ATAATAATAACAATA
Found at i:28108192 original size:2 final size:2
Alignment explanation
Indices: 28108185--28108220 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28108175 GCATGATACA
28108185 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
28108221 NNNNNNNNNN
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:28108471 original size:17 final size:16
Alignment explanation
Indices: 28108441--28108482 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
28108431 TATTTTTTTG
28108441 TTTTATTATT-ATTTAA
1 TTTTATT-TTCATTTAA
*
28108457 TTATTATTTTCATTTTA
1 TT-TTATTTTCATTTAA
28108474 TTTTATTTT
1 TTTTATTTT
28108483 TTATTATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTTTCATTTAA
Found at i:28108479 original size:27 final size:27
Alignment explanation
Indices: 28108441--28108522 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 27
28108431 TATTTTTTTG
28108441 TTTTATTATTATTTAATTATTATTTTCA-
1 TTTTATT-TTATTTAATTATTATTTT-AT
* **
28108469 TTTTATTTTATTT-TTTATTATCATAT
1 TTTTATTTTATTTAATTATTATTTTAT
28108495 TTTCTATTTTATTTCTAATTATTATTTT
1 TTT-TATTTTA-TT-TAATTATTATTTT
28108523 TTCGTACTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
25 1 0.02
26 11 0.26
27 13 0.30
28 9 0.21
29 1 0.02
30 8 0.19
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTATTTTATTTAATTATTATTTTAT
Found at i:28108486 original size:12 final size:13
Alignment explanation
Indices: 28108441--28108524 Score: 66
Period size: 14 Copynumber: 6.3 Consensus size: 13
28108431 TATTTTTTTG
28108441 TTTTATTATTATT
1 TTTTATTATTATT
*
28108454 TAATTATTATT-TT
1 T-TTTATTATTATT
28108467 CATTTTATT-TTATT
1 --TTTTATTATTATT
28108481 TTTTATTATCATATT
1 TTTTATTAT--TATT
*
28108496 TTCTATT-TTATT
1 TTTTATTATTATT
* *
28108508 TCTAATTATTATT
1 TTTTATTATTATT
28108521 TTTT
1 TTTT
28108525 CGTACTTTAC
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
12 15 0.27
13 13 0.24
14 16 0.29
15 11 0.20
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTATTATT
Found at i:28108486 original size:23 final size:23
Alignment explanation
Indices: 28108434--28108521 Score: 62
Period size: 23 Copynumber: 4.0 Consensus size: 23
28108424 AATTGTCTAT
*
28108434 TTTTTTGTTTT-ATTATTATTTA
1 TTTTTTATTTTCATTATTATTTA
* *
28108456 ATTATTATTTTCATT-TTATTTTA
1 TTTTTTATTTTCATTATTA-TTTA
*
28108479 TTTTTTATTATCA-TATT-TTCTA
1 TTTTTTATTTTCATTATTATT-TA
*
28108501 --TTTTATTTCTAATTATTATTT
1 TTTTTTATTT-TCATTATTATTT
28108522 TTTCGTACTT
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
20 7 0.14
21 4 0.08
22 19 0.37
23 21 0.41
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.72
Consensus pattern (23 bp):
TTTTTTATTTTCATTATTATTTA
Found at i:28108497 original size:20 final size:18
Alignment explanation
Indices: 28108457--28108524 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 18
28108447 TATTATTTAA
28108457 TTATTATTTTCATTT-TATT
1 TTATT-TTTT-ATTTCTATT
28108476 TTATTTTTTATTATCATATT
1 TTATTTTTTATT-TC-TATT
* *
28108496 TTCTATTTTATTTCTAATT
1 TTATTTTTTATTTCT-ATT
28108515 ATTATTTTTT
1 -TTATTTTTT
28108525 CGTACTTTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 3 0.08
18 6 0.15
19 10 0.25
20 21 0.52
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTTTTATTTCTATT
Found at i:28108524 original size:27 final size:27
Alignment explanation
Indices: 28108454--28108525 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
28108444 TATTATTATT
* *
28108454 TAATTATTATTTTCATTTTATTTTATTTT
1 TAATTATTATTTT--TTCTATTTTATTTC
* * *
28108483 TTATTATCATATTTTCTATTTTATTTC
1 TAATTATTATTTTTTCTATTTTATTTC
28108510 TAATTATTATTTTTTC
1 TAATTATTATTTTTTC
28108526 GTACTTTACA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 25 0.71
29 10 0.29
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (27 bp):
TAATTATTATTTTTTCTATTTTATTTC
Found at i:28108656 original size:17 final size:16
Alignment explanation
Indices: 28108625--28108673 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
28108615 AAAAATTTTA
28108625 TTATTATTTTT-TATT
1 TTATTATTTTTATATT
28108640 TTATCTATTTTTATATTT
1 TTAT-TATTTTTATA-TT
*
28108658 TTATTATTATTATATT
1 TTATTATTTTTATATT
28108674 ATTTTTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.13
16 9 0.30
17 11 0.37
18 6 0.20
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTATTTTTATATT
Found at i:28108964 original size:23 final size:23
Alignment explanation
Indices: 28108938--28109005 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
28108928 ATTTGAATTA
28108938 TCTTTATTTATTATTTTTATCCC
1 TCTTTATTTATTATTTTTATCCC
* * ***
28108961 TCTTTTTTTTATTTTTTTCTATTGT
1 TC-TTTATTTATTATTTT-TATCCC
*
28108986 TATTTATTTATTATTTTTAT
1 TCTTTATTTATTATTTTTAT
28109006 TGAATAACTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
23 5 0.14
24 26 0.74
25 4 0.11
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (23 bp):
TCTTTATTTATTATTTTTATCCC
Found at i:28110653 original size:1 final size:1
Alignment explanation
Indices: 28110649--28110740 Score: 58
Period size: 1 Copynumber: 92.0 Consensus size: 1
28110639 AGTTTTTTCA
* * * * * * * * * *
28110649 TTTTTTTTTTTTATTTTTTTTTGTTTGTTTGTTTTTTTTTGTGTTTTTATTATATTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
28110714 GTTTGTTTTTTGTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
28110741 AATGAACTTC
Statistics
Matches: 63, Mismatches: 28, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.04, C:0.00, G:0.11, T:0.85
Consensus pattern (1 bp):
T
Found at i:28110660 original size:14 final size:13
Alignment explanation
Indices: 28110641--28110740 Score: 76
Period size: 13 Copynumber: 7.4 Consensus size: 13
28110631 CTTACCAAAG
*
28110641 TTTTTTCATTTTT
1 TTTTTTTATTTTT
28110654 TTTTTTTATTTTT
1 TTTTTTTATTTTT
*
28110667 TTTTGTTTGTTTGTT
1 TTTT-TTTATTT-TT
* *
28110682 TTTTTTTGTGTTT
1 TTTTTTTATTTTT
* *
28110695 TTATTATATTTTT
1 TTTTTTTATTTTT
28110708 TGTTTTGTT-TGTTTT
1 T-TTTT-TTAT-TTTT
* *
28110723 TTGTTTTGTTTTT
1 TTTTTTTATTTTT
28110736 TTTTT
1 TTTTT
28110741 AATGAACTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
13 38 0.54
14 20 0.29
15 12 0.17
ACGTcount: A:0.05, C:0.01, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTTTATTTTT
Found at i:28110696 original size:39 final size:39
Alignment explanation
Indices: 28110640--28110738 Score: 123
Period size: 39 Copynumber: 2.5 Consensus size: 39
28110630 TCTTACCAAA
* *
28110640 GTTTTTTCATTTT-TTTTTTTTAT-TTTTTTTTGTTTGTTT
1 GTTTTTT-GTTTTGTTTTTTTTATATTTTTTGT-TTTGTTT
*
28110679 GTTTTTT-TTTGTGTTTTTATTATATTTTTTGTTTTGTTT
1 GTTTTTTGTTT-TGTTTTTTTTATATTTTTTGTTTTGTTT
28110718 GTTTTTTGTTTTGTTTTTTTT
1 GTTTTTTGTTTTGTTTTTTTT
28110739 TTAATGAACT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
37 3 0.06
38 1 0.02
39 39 0.74
40 10 0.19
ACGTcount: A:0.05, C:0.01, G:0.11, T:0.83
Consensus pattern (39 bp):
GTTTTTTGTTTTGTTTTTTTTATATTTTTTGTTTTGTTT
Found at i:28110824 original size:37 final size:38
Alignment explanation
Indices: 28110770--28111115 Score: 464
Period size: 38 Copynumber: 9.2 Consensus size: 38
28110760 AGGTAATGAC
* * * ** *
28110770 ACTTTTAAGAATAAACTCCGCAAAATTGAGGCAACGTA
1 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
* * *
28110808 AC-TTTAAAAATGAACTCTTCAAAGCTGAAGTAACGAA
1 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
* *
28110845 ACTTTTAAAAATGAATTCTTCAAAGCTGAGGCAACGAA
1 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
*
28110883 ACTTTT-AAAATGAACTCCTCAAAGCTAAGGCAACGAA
1 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
* *
28110920 ACTTTT-AAAATGAACTCCTCAAAACTGAGGCAACGAG
1 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
* *
28110957 ACTTTTAAAAATAAACTCCTCAAAGCTGAGGCAACAAA
1 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
* * *
28110995 ACTTTTAAAAATGAACTCCTTAAAACTGAGGTAACGAA
1 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
* *
28111033 ACTCTTAAAAATGAACTCCTCAAAGCTGAGACAACGAA
1 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
*
28111071 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGTAACGAA
1 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
28111109 ACCTTTT
1 A-CTTTT
28111116 TTTCTTTTTT
Statistics
Matches: 270, Mismatches: 35, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
37 96 0.36
38 169 0.63
39 5 0.02
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (38 bp):
ACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAACGAA
Found at i:28111043 original size:76 final size:75
Alignment explanation
Indices: 28110770--28111110 Score: 468
Period size: 75 Copynumber: 4.5 Consensus size: 75
28110760 AGGTAATGAC
* * * * * *
28110770 ACTTTTAAGAATAAACTCCGCAAAATTGAGGCAACGTAACTTTAAAAATGAACTCTTCAAAGCTG
1 ACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAGCTG
* *
28110835 AAGTAACGAA
66 AGGCAACGAA
* * * * *
28110845 ACTTTTAAAAATGAATTCTTCAAAGCTGAGGCAACGAAACTTTTAAAATGAACTCCTCAAAGCTA
1 ACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAGCTG
28110910 AGGCAACGAA
66 AGGCAACGAA
* *
28110920 ACTTTT-AAAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTAAAAATAAACTCCTCAAAGCT
1 ACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC-TTTAAAAATGAACTCCTCAAAGCT
*
28110984 GAGGCAACAAA
65 GAGGCAACGAA
* *
28110995 ACTTTTAAAAATGAACTCCTTAAAACTGAGGTAACGAAACTCTTAAAAATGAACTCCTCAAAGCT
1 ACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACT-TTAAAAATGAACTCCTCAAAGCT
*
28111060 GAGACAACGAA
65 GAGGCAACGAA
* *
28111071 ACTTTTAAAAATGAACTCCTCAAAGCTGAGGTAACGAAAC
1 ACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAAC
28111111 CTTTTTTTCT
Statistics
Matches: 234, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
74 29 0.12
75 106 0.45
76 99 0.42
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (75 bp):
ACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTTTAAAAATGAACTCCTCAAAGCTG
AGGCAACGAA
Found at i:28121635 original size:14 final size:15
Alignment explanation
Indices: 28121616--28121645 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28121606 TAAAAGCAAT
28121616 AAAAT-AACAAATGC
1 AAAATAAACAAATGC
28121630 AAAATAAACAAATGC
1 AAAATAAACAAATGC
28121645 A
1 A
28121646 CTAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAATAAACAAATGC
Found at i:28122605 original size:11 final size:11
Alignment explanation
Indices: 28122587--28122669 Score: 73
Period size: 11 Copynumber: 7.4 Consensus size: 11
28122577 TTATTTTTTG
28122587 TTTTATTATTA
1 TTTTATTATTA
*
28122598 TTTAATTATTA
1 TTTTATTATTA
28122609 TTTTTATT-TTA
1 -TTTTATTATTA
*
28122620 TTTTATTATTT
1 TTTTATTATTA
28122631 TTTTATCATATT-
1 TTTTAT--TATTA
*
28122643 TTCTATT-TTA
1 TTTTATTATTA
28122653 TTTCTAATTATTA
1 TTT-T-ATTATTA
28122666 TTTT
1 TTTT
28122670 TTCGTACTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
9 2 0.03
10 10 0.17
11 22 0.37
12 15 0.25
13 10 0.17
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:28122629 original size:33 final size:33
Alignment explanation
Indices: 28122582--28122668 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
28122572 ATTGTTTATT
* *
28122582 TTTTGTTTTATTATTATTTAATTATTATTTT-TA
1 TTTTATTTTATTATTATTTAATCA-TATTTTCTA
* *
28122615 TTTTATTTTATTATTTTTTTATCATATTTTCTA
1 TTTTATTTTATTATTATTTAATCATATTTTCTA
28122648 TTTTATTTCTAATTATTATTT
1 TTTTATTT-T-ATTATTATTT
28122669 TTTCGTACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 6 0.13
33 30 0.65
34 1 0.02
35 9 0.20
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.72
Consensus pattern (33 bp):
TTTTATTTTATTATTATTTAATCATATTTTCTA
Found at i:28122670 original size:19 final size:20
Alignment explanation
Indices: 28122602--28122670 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
28122592 TTATTATTTA
28122602 ATTATTATTTTTATTT-TAT
1 ATTATTATTTTTATTTCTAT
*
28122621 TTTATTATTTTT-TTATC-AT
1 ATTATTATTTTTATT-TCTAT
*
28122640 ATT-TTCTATTTTATTTCTA-
1 ATTATTAT-TTTTATTTCTAT
28122659 ATTATTATTTTT
1 ATTATTATTTTT
28122671 TCGTACTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
18 5 0.12
19 29 0.73
20 6 0.15
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTATTATTTTTATTTCTAT
Found at i:28122797 original size:15 final size:14
Alignment explanation
Indices: 28122768--28122840 Score: 73
Period size: 15 Copynumber: 5.3 Consensus size: 14
28122758 GAATAAAAAA
28122768 TTTTATTAT-TATT
1 TTTTATTATATATT
28122781 TTTTATTATACTATT
1 TTTTATTATA-TATT
*
28122796 TTTTATTTTATATAT
1 TTTTATTATATAT-T
28122811 TTTTA-TAT-T-TT
1 TTTTATTATATATT
*
28122822 TATTATTATTATATT
1 TTTTATTA-TATATT
28122837 TTTT
1 TTTT
28122841 TGTAAGCAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
11 5 0.10
12 3 0.06
13 11 0.22
14 6 0.12
15 24 0.49
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATTATATATT
Found at i:28122798 original size:16 final size:15
Alignment explanation
Indices: 28122768--28122819 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
28122758 GAATAAAAAA
28122768 TTTTATTAT-TA-TT
1 TTTTATTATATATTT
28122781 TTTTATTATACTATTT
1 TTTTATTATA-TATTT
*
28122797 TTTATTTTATATATTT
1 TTT-TATTATATATTT
*
28122813 TTATATT
1 TTTTATT
28122820 TTTATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 9 0.28
15 5 0.16
16 12 0.38
17 6 0.19
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATTATATATTT
Found at i:28122819 original size:8 final size:8
Alignment explanation
Indices: 28122792--28122839 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
28122782 TTTATTATAC
28122792 TATTTTT-
1 TATTTTTA
28122799 TATTTTATA
1 TATTTT-TA
28122808 TATTTTTA
1 TATTTTTA
28122816 TATTTTTA
1 TATTTTTA
*
28122824 TTATTATTA
1 -TATTTTTA
28122833 TATTTTT
1 TATTTTT
28122840 TTGTAAGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
7 6 0.17
8 17 0.47
9 13 0.36
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTTA
Found at i:28122839 original size:17 final size:17
Alignment explanation
Indices: 28122770--28122839 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 17
28122760 ATAAAAAATT
28122770 TTATTATTAT-TTTTTA
1 TTATTATTATATTTTTA
* *
28122786 TTATACTATTTTTTATTTTA
1 TTAT--TATTATAT-TTTTA
*
28122806 TATATTTTTATATTTTTA
1 T-TATTATTATATTTTTA
28122824 TTATTATTATATTTTT
1 TTATTATTATATTTTT
28122840 TTGTAAGCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
16 4 0.09
17 14 0.32
18 11 0.25
19 6 0.14
20 6 0.14
21 3 0.07
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTATTATATTTTTA
Found at i:28123167 original size:13 final size:13
Alignment explanation
Indices: 28123102--28123167 Score: 55
Period size: 13 Copynumber: 4.9 Consensus size: 13
28123092 ATATATTTGA
*
28123102 ATTATCTTTATTT
1 ATTATTTTTATTT
*
28123115 ATTATTTTTATCCCT
1 ATTATTTTTAT--TT
*
28123130 CTT-TTTTT-TTCT
1 ATTATTTTTATT-T
28123142 ATTATTATTTATTT
1 ATTATT-TTTATTT
28123156 ATTATTTTTATT
1 ATTATTTTTATT
28123168 GAATAACTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
12 3 0.07
13 19 0.45
14 15 0.36
15 5 0.12
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTATTTTTATTT
Found at i:28123996 original size:12 final size:12
Alignment explanation
Indices: 28123979--28124003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28123969 GATTGACTTT
28123979 TCTTTTTTTTTC
1 TCTTTTTTTTTC
28123991 TCTTTTTTTTTC
1 TCTTTTTTTTTC
28124003 T
1 T
28124004 TCTCTTTATC
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTTTTTTTTC
Found at i:28124001 original size:15 final size:15
Alignment explanation
Indices: 28123981--28124010 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28123971 TTGACTTTTC
28123981 TTTTTTT-TTCTCTT
1 TTTTTTTCTTCTCTT
28123995 TTTTTTTCTTCTCTT
1 TTTTTTTCTTCTCTT
28124010 T
1 T
28124011 ATCCGGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTCTTCTCTT
Found at i:28124388 original size:17 final size:16
Alignment explanation
Indices: 28124340--28124389 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
28124330 ATCGGCGATA
*
28124340 TTTTTTGTTTGTGTT-
1 TTTTTTTTTTGTGTTG
*
28124355 TTTTTTTTCTT-TTTTG
1 TTTTTTTT-TTGTGTTG
28124371 TTTTTTTTTTGTGGTTG
1 TTTTTTTTTTGT-GTTG
28124388 TT
1 TT
28124390 CTCGGTTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 12 0.43
16 11 0.39
17 5 0.18
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTGTGTTG
Found at i:28132156 original size:16 final size:16
Alignment explanation
Indices: 28132137--28132167 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28132127 AGCATTATGG
28132137 CTTTCTTTTTCTTTTT
1 CTTTCTTTTTCTTTTT
*
28132153 CTTTTTTTTTCTTTT
1 CTTTCTTTTTCTTTT
28132168 GGTGGTGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTTCTTTTTCTTTTT
Found at i:28135058 original size:7 final size:7
Alignment explanation
Indices: 28135046--28135077 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
28135036 TTTTTTTAAA
28135046 CCAAGAT
1 CCAAGAT
28135053 CCAAGAT
1 CCAAGAT
28135060 CCAAGAT
1 CCAAGAT
28135067 CCAAGAT
1 CCAAGAT
28135074 CCAA
1 CCAA
28135078 AAGCCAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.31, G:0.12, T:0.12
Consensus pattern (7 bp):
CCAAGAT
Found at i:28141702 original size:26 final size:28
Alignment explanation
Indices: 28141672--28141770 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 28
28141662 TTTTATTTTT
* *
28141672 TAAATATTAATAATTTATAA-TTAATTA
1 TAAATATTAATAATTAATAATTTAAATA
28141699 -AAATATTAATAATTAATAATTTAAATA
1 TAAATATTAATAATTAATAATTTAAATA
* *
28141726 TAAATATT-TTAA-T-ATAATTTAATTA
1 TAAATATTAATAATTAATAATTTAAATA
*
28141751 CT-AATATT-TTAATTAATAAT
1 -TAAATATTAATAATTAATAAT
28141771 ATTTTATTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
25 21 0.33
26 21 0.33
27 14 0.22
28 7 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
TAAATATTAATAATTAATAATTTAAATA
Found at i:28141748 original size:40 final size:41
Alignment explanation
Indices: 28141704--28141790 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
28141694 AATTAAAATA
*
28141704 TTAATAATTAATAATTTAAAT-ATAAATATTTTA-ATATAAT
1 TTAATAACTAATAATTTAAATAAT-AATATTTTATATATAAT
* * * *
28141744 TTAATTACTAATATTTTAATTAATAATATTTTATTTATAAT
1 TTAATAACTAATAATTTAAATAATAATATTTTATATATAAT
28141785 TTAATA
1 TTAATA
28141791 TTATTATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
40 26 0.67
41 13 0.33
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (41 bp):
TTAATAACTAATAATTTAAATAATAATATTTTATATATAAT
Found at i:28141928 original size:15 final size:15
Alignment explanation
Indices: 28141669--28141928 Score: 77
Period size: 15 Copynumber: 17.5 Consensus size: 15
28141659 TTATTTTATT
28141669 TTTTAAATATTAATAA
1 TTTTAAATATTAAT-A
* *
28141685 TTTATAATTAATTAAAA
1 TTT-TAAAT-ATTAATA
*
28141702 TATT-AATAATTAATA
1 TTTTAAAT-ATTAATA
* *
28141717 ATTTAAATATAAATA
1 TTTTAAATATTAATA
28141732 TTTT-AATA-T-A-A
1 TTTTAAATATTAATA
* *
28141743 -TTTAATTACTAATA
1 TTTTAAATATTAATA
* *
28141757 TTTTAATTAATAATA
1 TTTTAAATATTAATA
28141772 TTTT--AT-TT-ATA
1 TTTTAAATATTAATA
* *
28141783 ATTT-AATATTATTA
1 TTTTAAATATTAATA
28141797 TTATTAAAATATTAATAA
1 TT-TT-AAATATTAAT-A
* *
28141815 TTTT--ATTTTTATA
1 TTTTAAATATTAATA
*
28141828 TTCATTAAAAATTTAATA
1 TT--TTAAATA-TTAATA
** * *
28141846 AATAAAACATTAATAA
1 TTTTAAATATTAAT-A
*
28141862 TTTAAAATATTAATCA
1 TTTTAAATATTAAT-A
*
28141878 TATT-AATATTAATAA
1 TTTTAAATATTAAT-A
28141893 TGTTT-AA-ATT-ATA
1 T-TTTAAATATTAATA
* *
28141906 TATAAAATATTAATA
1 TTTTAAATATTAATA
28141921 TTTTAAAT
1 TTTTAAAT
28141929 TTTATGAATA
Statistics
Matches: 180, Mismatches: 39, Indels: 51
0.67 0.14 0.19
Matches are distributed among these distances:
10 3 0.02
11 10 0.06
12 6 0.03
13 11 0.06
14 19 0.11
15 69 0.38
16 31 0.17
17 18 0.10
18 13 0.07
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAAATATTAATA
Found at i:28142075 original size:21 final size:22
Alignment explanation
Indices: 28142029--28142075 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
28142019 ACAAAACGCC
* *
28142029 GATCTGGCGCACCATGTGGCCT
1 GATCTGGCGCACCAGGTGGCCA
28142051 GATCTGGC-CACCACGGT-GCCA
1 GATCTGGCGCACCA-GGTGGCCA
28142072 GATC
1 GATC
28142076 AGCGCTTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.17, C:0.34, G:0.30, T:0.19
Consensus pattern (22 bp):
GATCTGGCGCACCAGGTGGCCA
Found at i:28157614 original size:79 final size:78
Alignment explanation
Indices: 28157504--28157728 Score: 238
Period size: 79 Copynumber: 2.8 Consensus size: 78
28157494 CATGTTGAAA
* * * *
28157504 ATTTACTTATTATAAATTATGTTAAAAATTTATTTGTTACATGTCATATTAAAAAAATATAGTTA
1 ATTTAATTATTA-CAATTATGTTAAAAATTTAATTGTTACACGTCATATTAAAAAAATATA-TTA
28157569 TTACACACTATGTTG
64 TTACACACTATGTTG
* * * *
28157584 ATTTAGTTATTACAATTTTGTTAAAAATTTAATTGTTACACATCATATTGAAAAAAATA-ATTGT
1 ATTTAATTATTACAATTATGTTAAAAATTTAATTGTTACACGTCATATT-AAAAAAATATATTAT
* *
28157648 TATATACTATGTTG
65 TACACACTATGTTG
* * * * * * *
28157662 ATTTAATTGTTACAAATCAGGTTACAAATTTAGTTGTTATACGTCAT-TTTAAAAAATATAATTA
1 ATTTAATTATTAC-AATTATGTTAAAAATTTAATTGTTACACGTCATATTAAAAAAATAT-ATTA
28157726 TTA
64 TTA
28157729 TCCATTATGT
Statistics
Matches: 121, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
77 8 0.07
78 28 0.23
79 65 0.54
80 20 0.17
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (78 bp):
ATTTAATTATTACAATTATGTTAAAAATTTAATTGTTACACGTCATATTAAAAAAATATATTATT
ACACACTATGTTG
Found at i:28157746 original size:55 final size:55
Alignment explanation
Indices: 28157682--28157806 Score: 160
Period size: 55 Copynumber: 2.3 Consensus size: 55
28157672 TACAAATCAG
* * * *
28157682 GTTACAAATTTAGTTGTTATACGTCATTTTAAAAAATATAATTATTATCCATTAT
1 GTTAAAAATTTAATTGTTATACATCATTTTAAAAAATATAATTATTATACATTAT
* * * *
28157737 GTTAAAAATTTAATTGTTATATATCATTTTGAAAAATGTAATTGTTATACATTAT
1 GTTAAAAATTTAATTGTTATACATCATTTTAAAAAATATAATTATTATACATTAT
* *
28157792 GTTGAAGATTTAATT
1 GTTAAAAATTTAATT
28157807 ATTACATGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (55 bp):
GTTAAAAATTTAATTGTTATACATCATTTTAAAAAATATAATTATTATACATTAT
Found at i:28157751 original size:27 final size:27
Alignment explanation
Indices: 28157495--28157840 Score: 104
Period size: 27 Copynumber: 12.9 Consensus size: 27
28157485 GTTACACGTC
* * *
28157495 ATGTTGAAAATTTACTTATTATAAATT
1 ATGTTAAAAATTTAATTATTATACATT
28157522 ATGTTAAAAATTT-ATT-TGT-TACATGT
1 ATGTTAAAAATTTAATTAT-TATACAT-T
* * * * *
28157548 CATATTAAAAAAATATAGTTATTACACACT
1 -ATGTT--AAAAATTTAATTATTATACATT
* * *
28157578 ATGTT---GATTTAGTTATTACA-ATT
1 ATGTTAAAAATTTAATTATTATACATT
* * * *
28157601 TTGTTAAAAATTTAATTGTTACACATC
1 ATGTTAAAAATTTAATTATTATACATT
* ** * * *
28157628 ATATTGAAAAAAATAATTGTTATATACT
1 ATGTT-AAAAATTTAATTATTATACATT
* * * * *
28157656 ATGTT---GATTTAATTGTTACAAATC
1 ATGTTAAAAATTTAATTATTATACATT
* * * * * *
28157680 AGGTTACAAATTTAGTTGTTATACGTC
1 ATGTTAAAAATTTAATTATTATACATT
* * *
28157707 ATTTTAAAAAATATAATTATTATCCATT
1 ATGTT-AAAAATTTAATTATTATACATT
* * *
28157735 ATGTTAAAAATTTAATTGTTATATATC
1 ATGTTAAAAATTTAATTATTATACATT
* * *
28157762 ATTTTGAAAAATGTAATTGTTATACATT
1 ATGTT-AAAAATTTAATTATTATACATT
* *
28157790 ATGTTGAAGATTTAATTA-T-TACATGGT
1 ATGTTAAAAATTTAATTATTATACAT--T
* *
28157817 ATTTTGAAAAATTTAATTGTTATA
1 ATGTT-AAAAATTTAATTATTATA
28157841 TGTTATGATG
Statistics
Matches: 229, Mismatches: 67, Indels: 43
0.68 0.20 0.13
Matches are distributed among these distances:
23 6 0.03
24 29 0.13
25 10 0.04
26 17 0.07
27 73 0.32
28 72 0.31
29 12 0.05
30 6 0.03
31 4 0.02
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (27 bp):
ATGTTAAAAATTTAATTATTATACATT
Found at i:28157821 original size:55 final size:55
Alignment explanation
Indices: 28157705--28157840 Score: 166
Period size: 55 Copynumber: 2.5 Consensus size: 55
28157695 TTGTTATACG
* * * * *
28157705 TCATTTTAAAAAATATAATTATTATCCATTATGTTAAAAATTTAATTGTTATATA
1 TCATTTTGAAAAATATAATTGTTATACATTATGTTAAAAATTTAATTATTACATA
* * * *
28157760 TCATTTTGAAAAATGTAATTGTTATACATTATGTTGAAGATTTAATTATTACATGG
1 TCATTTTGAAAAATATAATTGTTATACATTATGTTAAAAATTTAATTATTACAT-A
*
28157816 T-ATTTTGAAAAATTTAATTGTTATA
1 TCATTTTGAAAAATATAATTGTTATA
28157841 TGTTATGATG
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
55 69 0.99
56 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (55 bp):
TCATTTTGAAAAATATAATTGTTATACATTATGTTAAAAATTTAATTATTACATA
Found at i:28157852 original size:28 final size:28
Alignment explanation
Indices: 28157602--28157855 Score: 146
Period size: 28 Copynumber: 9.4 Consensus size: 28
28157592 ATTACAATTT
* * *
28157602 TGTT-AAAAATTTAATTGTTACACATCA
1 TGTTGAAAAATTTAATTGTTATATATTA
* ** *
28157629 TATTGAAAAAAATAATTGTTATATACTA
1 TGTTGAAAAATTTAATTGTTATATATTA
* * *
28157657 TGTTG----ATTTAATTGTTACAAATCA
1 TGTTGAAAAATTTAATTGTTATATATTA
* * * ** *
28157681 GGTT-ACAAATTTAGTTGTTATACGTCA
1 TGTTGAAAAATTTAATTGTTATATATTA
* * * * **
28157708 TTTTAAAAAATATAATTATTATCCATTA
1 TGTTGAAAAATTTAATTGTTATATATTA
*
28157736 TGTT-AAAAATTTAATTGTTATATATCA
1 TGTTGAAAAATTTAATTGTTATATATTA
* * *
28157763 TTTTGAAAAATGTAATTGTTATACATTA
1 TGTTGAAAAATTTAATTGTTATATATTA
* * * **
28157791 TGTTG-AAGATTTAATTATTACATGGTA
1 TGTTGAAAAATTTAATTGTTATATATTA
* *
28157818 TTTTGAAAAATTTAATTGTTATATGTTA
1 TGTTGAAAAATTTAATTGTTATATATTA
*
28157846 TGATGAAAAA
1 TGTTGAAAAA
28157856 ATTATTACAC
Statistics
Matches: 166, Mismatches: 53, Indels: 15
0.71 0.23 0.06
Matches are distributed among these distances:
24 16 0.10
27 60 0.36
28 90 0.54
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.44
Consensus pattern (28 bp):
TGTTGAAAAATTTAATTGTTATATATTA
Found at i:28167327 original size:28 final size:28
Alignment explanation
Indices: 28167295--28167358 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
28167285 TAGGGTAGGT
28167295 TTCGGGTAGTGATTTCACTACCCGAAGG
1 TTCGGGTAGTGATTTCACTACCCGAAGG
28167323 TTCGGGTAGTGATTTCACTACCCGAAGG
1 TTCGGGTAGTGATTTCACTACCCGAAGG
28167351 TTCGGGTA
1 TTCGGGTA
28167359 TCATTCTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (28 bp):
TTCGGGTAGTGATTTCACTACCCGAAGG
Found at i:28175782 original size:71 final size:72
Alignment explanation
Indices: 28175679--28175846 Score: 171
Period size: 71 Copynumber: 2.3 Consensus size: 72
28175669 CCAAGTTTTG
** * * *
28175679 GAAAGCAAGTTCAAAAGTATCAACACCAAAGCTT-CAAGGTATCAAGACTTCA-CTTTAAATTGC
1 GAAAGCAAGTTCAAAAGTATTGAGAACAAAGCTTCCAA-GTATCAAGACTTCATCTTCAAATTGC
28175742 AAATTCCA
65 AAATTCCA
* ** * *
28175750 GAAAGCAAGTTCAAAAGTATTGAGAACTAAGCTTCCAAGTATTGAGACTTCATCTTCAGATTTCA
1 GAAAGCAAGTTCAAAAGTATTGAGAACAAAGCTTCCAAGTATCAAGACTTCATCTTCAAATTGCA
*
28175815 ATTTCCA
66 AATTCCA
* * *
28175822 -AAGAGCAAGTGCTAGAGTATTGAGA
1 GAA-AGCAAGTTCAAAAGTATTGAGA
28175847 CTCATTTTCA
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
71 43 0.54
72 37 0.46
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (72 bp):
GAAAGCAAGTTCAAAAGTATTGAGAACAAAGCTTCCAAGTATCAAGACTTCATCTTCAAATTGCA
AATTCCA
Found at i:28176614 original size:35 final size:36
Alignment explanation
Indices: 28176575--28176649 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
28176565 TTGATCCTTA
28176575 AAAAGA-TTGG-TGTAAAAGGTTAAG-TCTAAGTCTTG
1 AAAAGACTTGGTTGT-AAAGGTTAAGCT-TAAGTCTTG
* *
28176610 AAAAGACTTGGTTGTAAAGGTTATGCTTGAGTCTTG
1 AAAAGACTTGGTTGTAAAGGTTAAGCTTAAGTCTTG
28176646 AAAA
1 AAAA
28176650 AGTAGTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 6 0.17
36 25 0.71
37 4 0.11
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (36 bp):
AAAAGACTTGGTTGTAAAGGTTAAGCTTAAGTCTTG
Found at i:28189343 original size:18 final size:18
Alignment explanation
Indices: 28189320--28189357 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28189310 TGAGACATTG
*
28189320 TTTATTTATTTTGTTTTA
1 TTTATTTATTTTGTTATA
28189338 TTTATTTATTTTGTTATA
1 TTTATTTATTTTGTTATA
28189356 TT
1 TT
28189358 GCTGATGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTATTTATTTTGTTATA
Found at i:28195443 original size:12 final size:12
Alignment explanation
Indices: 28195428--28195452 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28195418 ACATGTCATA
28195428 TCATACATACAT
1 TCATACATACAT
28195440 TCATACATACAT
1 TCATACATACAT
28195452 T
1 T
28195453 TTCAAAAGGC
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCATACATACAT
Found at i:28200450 original size:2 final size:2
Alignment explanation
Indices: 28200443--28200483 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
28200433 GCACTATTAC
28200443 AT AT AT AT AT AT AT AT AT AT AT AT A- 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
28200484 GATCATATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28201602 original size:16 final size:18
Alignment explanation
Indices: 28201566--28201603 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
28201556 TTAGGCCTCA
*
28201566 AATTGTTATAGATATCAT
1 AATTGTTATAGATAACAT
28201584 AATT-TTATA-ATAACAT
1 AATTGTTATAGATAACAT
28201600 AATT
1 AATT
28201604 AATTAAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 5 0.26
18 4 0.21
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTGTTATAGATAACAT
Found at i:28202398 original size:2 final size:2
Alignment explanation
Indices: 28202386--28202421 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
28202376 CAACAGAACT
*
28202386 TA TA TA CA TA TA TA TA TA TA TA -A 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 T
28202422 TGTAATTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:28205077 original size:32 final size:32
Alignment explanation
Indices: 28205036--28205100 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
28205026 ATCTTTTTGG
28205036 AGCATATTTAAAGGCACTTTTGACGCAATTGA
1 AGCATATTTAAAGGCACTTTTGACGCAATTGA
28205068 AGCATATTTAAAGGCACTTTTGACGCAATTGA
1 AGCATATTTAAAGGCACTTTTGACGCAATTGA
28205100 A
1 A
28205101 AGACACAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (32 bp):
AGCATATTTAAAGGCACTTTTGACGCAATTGA
Found at i:28205548 original size:23 final size:23
Alignment explanation
Indices: 28205518--28205567 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
28205508 TCTGCTATGC
28205518 TTTC-GATTTCTCTCTCCTACAT
1 TTTCAGATTTCTCTCTCCTACAT
* *
28205540 TTTCAGATTTCTCTTTCTTACAT
1 TTTCAGATTTCTCTCTCCTACAT
28205563 TTTCA
1 TTTCA
28205568 AAACACCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.16, C:0.26, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTCAGATTTCTCTCTCCTACAT
Found at i:28206000 original size:29 final size:30
Alignment explanation
Indices: 28205958--28206026 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 30
28205948 TGAATATGTC
28205958 GTGTAACAACAATA-TTTTTTCAACATGGT
1 GTGTAACAACAATATTTTTTTCAACATGGT
*
28205987 GTGTAACAATAATATTTTTTTTCAACATGGT
1 GTGTAACAACAATA-TTTTTTTCAACATGGT
28206018 GTGTAACAA
1 GTGTAACAA
28206027 ACTTTTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 13 0.35
31 24 0.65
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (30 bp):
GTGTAACAACAATATTTTTTTCAACATGGT
Found at i:28206058 original size:26 final size:25
Alignment explanation
Indices: 28205965--28206075 Score: 80
Period size: 26 Copynumber: 4.2 Consensus size: 25
28205955 GTCGTGTAAC
* *
28205965 AACAATATTTTTTCAACATGGTGTGT
1 AACAA-ATTTTTTTAACATGGCGTGT
*
28205991 AACAATAATATTTTTTTTCAACATGGTGTGT
1 AAC---AA-A-TTTTTTT-AACATGGCGTGT
*
28206022 AACAAACTTTTTTAACCATGGCGTGT
1 AACAAATTTTTTTAA-CATGGCGTGT
** *
28206048 AACATGTTTTTTT-ACATGACGTGT
1 AACAAATTTTTTTAACATGGCGTGT
28206072 AACA
1 AACA
28206076 GTAGTATTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
24 13 0.18
25 3 0.04
26 28 0.39
27 1 0.01
28 2 0.03
29 4 0.06
30 6 0.08
31 15 0.21
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (25 bp):
AACAAATTTTTTTAACATGGCGTGT
Found at i:28206065 original size:24 final size:24
Alignment explanation
Indices: 28206002--28206075 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
28205992 ACAATAATAT
*
28206002 TTTTTTTCAACATGGTGTGTAACAAAC
1 TTTTTTT--ACATGGCGTGTAAC-AAC
* **
28206029 TTTTTTAACCATGGCGTGTAACATG
1 TTTTTTTA-CATGGCGTGTAACAAC
*
28206054 TTTTTTTACATGACGTGTAACA
1 TTTTTTTACATGGCGTGTAACA
28206076 GTAGTATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 13 0.32
25 9 0.22
26 12 0.30
27 6 0.15
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (24 bp):
TTTTTTTACATGGCGTGTAACAAC
Found at i:28206085 original size:26 final size:24
Alignment explanation
Indices: 28206038--28206086 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28206028 CTTTTTTAAC
* *
28206038 CATGGCGTGTAACATGTTTTTTTA
1 CATGACGTGTAACATGTATTTTTA
28206062 CATGACGTGTAACAGTAGTATTTTT
1 CATGACGTGTAACA-T-GTATTTTT
28206087 TTTCAACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 1 0.05
26 7 0.33
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.43
Consensus pattern (24 bp):
CATGACGTGTAACATGTATTTTTA
Found at i:28206096 original size:31 final size:28
Alignment explanation
Indices: 28205972--28206104 Score: 100
Period size: 31 Copynumber: 4.8 Consensus size: 28
28205962 AACAACAATA
* *
28205972 TTTTTTCAACATGGTGTGTAACAATAATATT
1 TTTTTTCAACATGGCGTGTAAC-AT-AGA-T
* *
28206003 TTTTTTCAACATGGTGTGTAACA-A-AC
1 TTTTTTCAACATGGCGTGTAACATAGAT
28206029 TTTTTT-AACCATGGCGTGTAACAT-G-T
1 TTTTTTCAA-CATGGCGTGTAACATAGAT
*
28206055 TTTTTT--ACATGACGTGTAACAGTAGTATT
1 TTTTTTCAACATGGCGTGTAACA-TAG-A-T
*
28206084 TTTTTTCAACATGGCATGTAA
1 TTTTTTCAACATGGCGTGTAA
28206105 AAACCTAACC
Statistics
Matches: 86, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
24 13 0.15
25 4 0.05
26 26 0.30
27 1 0.01
28 1 0.01
29 7 0.08
30 1 0.01
31 33 0.38
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (28 bp):
TTTTTTCAACATGGCGTGTAACATAGAT
Found at i:28206141 original size:45 final size:45
Alignment explanation
Indices: 28206092--28206321 Score: 235
Period size: 45 Copynumber: 5.1 Consensus size: 45
28206082 TTTTTTTTCA
* *
28206092 ACATGGCATGTAAAAACCTAACCATGGCTTGTTACAGGTTTTTGT
1 ACATGGCATGTAAAAAGCTAACCATGGCTTGTCACAGGTTTTTGT
* *
28206137 ACATGGCATGTAACAAGCTAACCATAGCTTGTCACAGGTTTTTGT
1 ACATGGCATGTAAAAAGCTAACCATGGCTTGTCACAGGTTTTTGT
* * * * * **
28206182 ACATGACTTGTAACAAGCTAATCATGACTTGTCACATATTTTTGT
1 ACATGGCATGTAAAAAGCTAACCATGGCTTGTCACAGGTTTTTGT
* * * * * *
28206227 ATATAGCGTGTAACACGCTAACTATGGCTTGTCACAGGTTTTTGT
1 ACATGGCATGTAAAAAGCTAACCATGGCTTGTCACAGGTTTTTGT
* * ** * ** *
28206272 AAATGGCGTGTAGTAAGCTAACCGTAACTTGTCACAAGTTTTTGT
1 ACATGGCATGTAAAAAGCTAACCATGGCTTGTCACAGGTTTTTGT
28206317 ACATG
1 ACATG
28206322 ACTTGTCACA
Statistics
Matches: 153, Mismatches: 32, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 153 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (45 bp):
ACATGGCATGTAAAAAGCTAACCATGGCTTGTCACAGGTTTTTGT
Found at i:28206341 original size:23 final size:23
Alignment explanation
Indices: 28206298--28206344 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
28206288 GCTAACCGTA
28206298 ACTTGTCACAAGTTTTTGTACATG
1 ACTTGTCACAAG-TTTTGTACATG
28206322 ACTTGTCACATA-TTTTGTACATG
1 ACTTGTCACA-AGTTTTGTACATG
28206345 GCATGTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.50
24 10 0.45
25 1 0.05
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (23 bp):
ACTTGTCACAAGTTTTGTACATG
Found at i:28206383 original size:113 final size:114
Alignment explanation
Indices: 28206204--28206434 Score: 293
Period size: 113 Copynumber: 2.0 Consensus size: 114
28206194 ACAAGCTAAT
* * * * *
28206204 CATGACTTGTCACATATTTTTGTATATAGCGTGTAACACGCTAACTATGGCTTGTCACAGGTTTT
1 CATGACTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGGCTTGTCACAGATTTT
* * ** *
28206269 TGTAAATGGCGTGTAGTAAGCTAACCGTAACTTGTCACAAGTTTTTGTA
66 TGTAAATAGCATGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTA
* * *
28206318 CATGACTTGTCACATA-TTTTGTACATGGCATGTAACAAGCTTACCATGGCTTGTCACATATTTT
1 CATGACTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGGCTTGTCACAGATTTT
* * * * *
28206382 TGTACATAGCATGTAACACGCTAACCATGACTTGTCATAGGTTTTTGTA
66 TGTAAATAGCATGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTA
28206431 CATG
1 CATG
28206435 GCGTGTAACA
Statistics
Matches: 99, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
113 83 0.84
114 16 0.16
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (114 bp):
CATGACTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGGCTTGTCACAGATTTT
TGTAAATAGCATGTAACAAGCTAACCATAACTTGTCACAAGTTTTTGTA
Found at i:28206394 original size:45 final size:45
Alignment explanation
Indices: 28206318--28206478 Score: 193
Period size: 45 Copynumber: 3.6 Consensus size: 45
28206308 AGTTTTTGTA
*
28206318 CATGACTTGTCACATA-TTTTGTACATGGCATGTAACAAGCTTAC
1 CATGACTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAAC
* * *
28206362 CATGGCTTGTCACATATTTTTGTACATAGCATGTAACACGCTAAC
1 CATGACTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAAC
* ** * * *
28206407 CATGACTTGTCATAGGTTTTTGTACATGGCGTGTAACAAGCCAAA
1 CATGACTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAAC
28206452 CAT-AGCTTGTCACA-AGTTTTTGTACAT
1 CATGA-CTTGTCACATA-TTTTTGTACAT
28206479 TGCTTGTCAC
Statistics
Matches: 99, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
44 16 0.16
45 83 0.84
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (45 bp):
CATGACTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAAC
Found at i:28206483 original size:24 final size:24
Alignment explanation
Indices: 28206451--28206502 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
28206441 AACAAGCCAA
28206451 ACATAGCTTGTCACA-AGTTTTTGT
1 ACATAGCTTGTCACATA-TTTTTGT
*
28206475 ACATTGCTTGTCACATATTTTTGT
1 ACATAGCTTGTCACATATTTTTGT
28206499 ACAT
1 ACAT
28206503 GGCATGTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.44
Consensus pattern (24 bp):
ACATAGCTTGTCACATATTTTTGT
Found at i:28206508 original size:114 final size:114
Alignment explanation
Indices: 28206366--28206592 Score: 310
Period size: 114 Copynumber: 2.0 Consensus size: 114
28206356 GCTTACCATG
* * * *
28206366 GCTTGTCACATATTTTTGTACATAGCATGTAACACGCTAACCATGACTTGTCATAGGTTTTTGTA
1 GCTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGACTTGTCACAGATTTTTATA
* *
28206431 CATGGCGTGTAACAAGCCAAACATAGCTTGTCACAAGTTTTTGTACATT
66 CATAGCGTGTAACAAGCCAAACATAGCTTATCACAAGTTTTTGTACATT
* ** *
28206480 GCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACCATGGTTTGTCACATATTTTTATA
1 GCTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGACTTGTCACAGATTTTTATA
* * * * **
28206545 CATAGCGTGTAACACGCTAACCATGGCTTATCACGGGTTTTTGTACAT
66 CATAGCGTGTAACAAGCCAAACATAGCTTATCACAAGTTTTTGTACAT
28206593 AGCGTGTAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (114 bp):
GCTTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACCATGACTTGTCACAGATTTTTATA
CATAGCGTGTAACAAGCCAAACATAGCTTATCACAAGTTTTTGTACATT
Found at i:28206533 original size:45 final size:45
Alignment explanation
Indices: 28206480--28206634 Score: 195
Period size: 45 Copynumber: 3.4 Consensus size: 45
28206470 TTTGTACATT
* *
28206480 GCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACCATG
1 GCTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATG
* * *
28206525 GTTTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATG
1 GCTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATG
* *** * *
28206570 GCTTATCACGGGTTTTTGTACATAGCGTGTAAAAAGCTAACCATA
1 GCTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATG
28206615 GCTTGTCACA-AGTTTTTGTA
1 GCTTGTCACATA-TTTTTGTA
28206635 TATGGCTTAT
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 92 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (45 bp):
GCTTGTCACATATTTTTGTACATAGCGTGTAACAAGCTAACCATG
Found at i:28206564 original size:159 final size:159
Alignment explanation
Indices: 28206163--28206796 Score: 957
Period size: 159 Copynumber: 4.0 Consensus size: 159
28206153 GCTAACCATA
** * * * *
28206163 GCTTGTCACAGGTTTTTGTACATGACTTGTAACAAGCTAATCATGACTTGTCACATATTTTTGTA
1 GCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGTA
* * * **
28206228 TATAGCGTGTAACACGCTAACTATGGCTTGTCACAGGTTTTTGTAAATGGCGTGTAGTAAGCTAA
66 CATAGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAA
* *
28206293 CCGTAACTTGTCACAAGTTTTTGTACA-T
131 CCATAGCTTGTCACAAGTTTTTGTACATT
*
28206321 GACTTGTCACATA-TTTTGTACATGGCATGTAACAAGCTTACCATGGCTTGTCACATATTTTTGT
1 G-CTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGT
* * * *
28206385 ACATAGCATGTAACACGCTAACCATGACTTGTCATAGGTTTTTGTACATGGCGTGTAACAAGCCA
65 ACATAGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTA
*
28206450 AACATAGCTTGTCACAAGTTTTTGTACATT
130 ACCATAGCTTGTCACAAGTTTTTGTACATT
* *
28206480 GCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACCATGGTTTGTCACATATTTTTATA
1 GCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGTA
* * * *
28206545 CATAGCGTGTAACACGCTAACCATGGCTTATCACGGGTTTTTGTACATAGCGTGTAAAAAGCTAA
66 CATAGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAA
* *
28206610 CCATAGCTTGTCACAAGTTTTTGTATATG
131 CCATAGCTTGTCACAAGTTTTTGTACATT
* * * *
28206639 GCTTATCACGTATTTTTGTGCATGGCATGTAACAAGCTAACCGTGGCTTGTCACATATTTTTGTA
1 GCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGTA
*
28206704 CATAGAGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAA
66 CATAGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAA
28206769 CCATAGCTTGTCACAAGTTTTTGTACAT
131 CCATAGCTTGTCACAAGTTTTTGTACAT
28206797 GGCGTGTAAC
Statistics
Matches: 428, Mismatches: 45, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
158 139 0.32
159 289 0.68
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (159 bp):
GCTTGTCACATATTTTTGTACATGGCATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGTA
CATAGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAA
CCATAGCTTGTCACAAGTTTTTGTACATT
Done.