Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1787
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: 95630
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:8728 original size:1 final size:1
Alignment explanation
Indices: 8722--8818 Score: 68
Period size: 1 Copynumber: 97.0 Consensus size: 1
8712 GGCGTCCTCC
** ** ** ** *
8722 AAAAAAAAAAAAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAAAGGAAAAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
8787 AAAACAATAAAAAAACAAACAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8819 GGGGGTCCGG
Statistics
Matches: 74, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:8783 original size:27 final size:26
Alignment explanation
Indices: 8721--8818 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 26
8711 CGGCGTCCTC
8721 CAAAAAAAAA-AAAAAAA-AAAACGAAA
1 CAAAAAAAAACAAAAAAATAAAA--AAA
8747 -AAAATGAAAAACCAAAAAAA-AAAAAAA
1 CAAAA--AAAAA-CAAAAAAATAAAAAAA
*
8774 GGAAAAAAAAACAAAAACAATAAAAAAA
1 -CAAAAAAAAACAAAAA-AATAAAAAAA
*
8802 CAAACAAAAACAAAAAA
1 CAAAAAAAAACAAAAAA
8819 GGGGGTCCGG
Statistics
Matches: 62, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
25 4 0.06
26 7 0.11
27 29 0.47
28 7 0.11
29 15 0.24
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.02
Consensus pattern (26 bp):
CAAAAAAAAACAAAAAAATAAAAAAA
Found at i:8783 original size:43 final size:44
Alignment explanation
Indices: 8721--8820 Score: 136
Period size: 43 Copynumber: 2.3 Consensus size: 44
8711 CGGCGTCCTC
* *
8721 CAAAAAAAAAAA--AAAAAAAAACGAAAAA-AATGAAAAACCAAA
1 CAAAAAAAAAAAGGAAAAAAAAAC-AAAAACAATAAAAAAACAAA
8763 -AAAAAAAAAAAGGAAAAAAAAACAAAAACAATAAAAAAACAAA
1 CAAAAAAAAAAAGGAAAAAAAAACAAAAACAATAAAAAAACAAA
8806 CAAAAACAAAAAAGG
1 CAAAAA-AAAAAAGG
8821 GGGTCCGGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
41 11 0.22
42 5 0.10
43 22 0.43
44 5 0.10
45 8 0.16
ACGTcount: A:0.83, C:0.09, G:0.06, T:0.02
Consensus pattern (44 bp):
CAAAAAAAAAAAGGAAAAAAAAACAAAAACAATAAAAAAACAAA
Found at i:8799 original size:32 final size:33
Alignment explanation
Indices: 8721--8811 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 33
8711 CGGCGTCCTC
* *
8721 CAAAAAAAAAAAAAAAAAAAACGAAAAAAATGA
1 CAAAAACAAAAAAAAAAAAAACGAAAAAAATAA
* *
8754 -AAAACCAAAAAAAAAAAAAAGGAAAAAAA-AA
1 CAAAAACAAAAAAAAAAAAAACGAAAAAAATAA
* *
8785 CAAAAACAATAAAAAAACAAAC-AAAAA
1 CAAAAACAAAAAAAAAAAAAACGAAAAA
8812 CAAAAAAGGG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 6 0.12
32 43 0.88
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.02
Consensus pattern (33 bp):
CAAAAACAAAAAAAAAAAAAACGAAAAAAATAA
Found at i:10299 original size:29 final size:29
Alignment explanation
Indices: 10260--10385 Score: 130
Period size: 30 Copynumber: 4.3 Consensus size: 29
10250 TCACCCTTCA
*
10260 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
*
10289 AAAGCCCACAAGTCGGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* ***
10318 GAAAGCCCACAAGTTAGTGGCA--ACCTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
* ** *
10346 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTC
10376 AAAGCCCACA
1 AAAGCCCACA
10386 CAAGTCGGTG
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
27 19 0.24
28 3 0.04
29 27 0.34
30 31 0.39
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTC
Found at i:10315 original size:30 final size:30
Alignment explanation
Indices: 10260--10339 Score: 126
Period size: 29 Copynumber: 2.7 Consensus size: 30
10250 TCACCCTTCA
*
10260 AAAGTCCACAAGTCAGTGGCATTTTTTTC-
1 AAAGCCCACAAGTCAGTGGCATTTTTTTCG
*
10289 AAAGCCCACAAGTCGGTGGCATTTTTTTCG
1 AAAGCCCACAAGTCAGTGGCATTTTTTTCG
*
10319 AAAGCCCACAAGTTAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
10340 ACCTTCAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 27 0.59
30 19 0.41
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTCG
Found at i:10363 original size:27 final size:27
Alignment explanation
Indices: 10319--10413 Score: 91
Period size: 27 Copynumber: 3.3 Consensus size: 27
10309 ATTTTTTTCG
* *
10319 AAAGCCCACAAGTTAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
10346 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAATCAGTGGCAACC--TT-C
*
10376 AAAGCCCACACAAGTCGGTGGCAACCCTTC
1 AAAGCCCACA-AA-TCAGTGGCAA-CCTTC
*
10406 TAAGCCCA
1 AAAGCCCA
10414 ATATAGCTGG
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
27 21 0.38
29 2 0.04
30 19 0.34
31 4 0.07
32 8 0.14
33 2 0.04
ACGTcount: A:0.32, C:0.35, G:0.17, T:0.17
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:10365 original size:57 final size:60
Alignment explanation
Indices: 10286--10413 Score: 154
Period size: 57 Copynumber: 2.2 Consensus size: 60
10276 TGGCATTTTT
* * *** * *
10286 TTCAAAGCCCACAAGTCGGTGGCATTTTTTTCGAAAG-CC-CACAAGTTAGTGGCAA-CC
1 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
*
10343 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACACAAGTCGGTGGCAACCC
1 TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
*
10403 TTCTAAGCCCA
1 TTCAAAGCCCA
10414 ATATAGCTGG
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
57 31 0.53
58 2 0.03
59 14 0.24
60 12 0.20
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (60 bp):
TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
Found at i:10381 original size:30 final size:30
Alignment explanation
Indices: 10260--10404 Score: 118
Period size: 30 Copynumber: 4.9 Consensus size: 30
10250 TCACCCTTCA
* ** *
10260 AAAGTCCACAAGTCAGTGGCA-TTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *** *
10289 AAAGCCCACAAGTCGGTGGCATTTTTTTCG
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
* *
10319 AAAGCCCACAAGTTAGTGGCAACC--TT-C
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
10346 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
*
10376 AAAGCCCACACAAGTCGGTGGCAACCCTT
1 AAAG-CC-CACAAGTCAGTGGC-ACCCTT
10405 CTAAGCCCAA
Statistics
Matches: 94, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
27 21 0.22
28 2 0.02
29 21 0.22
30 30 0.32
31 2 0.02
32 12 0.13
33 6 0.06
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTCC
Found at i:10411 original size:30 final size:30
Alignment explanation
Indices: 10325--10413 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
10315 TTCGAAAGCC
*
10325 CACAAGTTAGTGGCAA-CCTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
10354 CA-AA-TCAGTGGC-ACCCTTTTCCAAAGCCCA
1 CACAAGTCAGTGGCAACCC--TT-CAAAGCCCA
* *
10384 CACAAGTCGGTGGCAACCCTTCTAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
10414 ATATAGCTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
26 1 0.02
27 9 0.18
28 2 0.04
29 4 0.08
30 19 0.38
31 4 0.08
32 7 0.14
33 4 0.08
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.18
Consensus pattern (30 bp):
CACAAGTCAGTGGCAACCCTTCAAAGCCCA
Found at i:10468 original size:49 final size:49
Alignment explanation
Indices: 10406--10743 Score: 340
Period size: 49 Copynumber: 7.0 Consensus size: 49
10396 GCAACCCTTC
* *
10406 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
10455 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
10504 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * *
10547 TAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
10590 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TTT-ATCTT
* * * * *
10642 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * * * *
10697 TAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
10744 ACTTTTCTCA
Statistics
Matches: 251, Mismatches: 26, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
43 80 0.32
44 1 0.00
48 1 0.00
49 85 0.34
50 1 0.00
51 2 0.01
52 38 0.15
53 2 0.01
54 5 0.02
55 36 0.14
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:10546 original size:21 final size:21
Alignment explanation
Indices: 10522--10589 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
10512 ATATAGCTGG
10522 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* *
10543 CCTTTAAGTC--CA-ATGTAGCTGA
1 CCTTGAA-TCAGCACAT-TGGC--A
10565 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
10586 CCTT
1 CCTT
10590 TAAGTCCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:10562 original size:43 final size:43
Alignment explanation
Indices: 10498--10633 Score: 245
Period size: 43 Copynumber: 3.2 Consensus size: 43
10488 TTGGCACCTT
10498 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
* *
10541 CACCTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
*
10584 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
10627 CACCTTT
1 CACCTTT
10634 TTCATCTTTA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 88 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (43 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG
Found at i:10665 original size:52 final size:51
Alignment explanation
Indices: 10587--10748 Score: 180
Period size: 52 Copynumber: 3.1 Consensus size: 51
10577 ACATTGGCAC
10587 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
* * * *
10638 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCA
1 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTT-TCA
* * * * * * *
10693 GCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA
1 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
10745 CTTT
1 CTTT
10749 TCTCATCATC
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
51 4 0.04
52 41 0.45
53 5 0.05
54 5 0.05
55 36 0.40
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (51 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCA
Found at i:10723 original size:55 final size:55
Alignment explanation
Indices: 10587--11050 Score: 379
Period size: 49 Copynumber: 8.7 Consensus size: 55
10577 ACATTGGCAC
*
10587 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTT-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * *
10639 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
10694 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
* *
10758 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * **
10810 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
10865 CTTTAAGCCCAATATCGTTGGCCTTGAATCACCATATTGGCA-CC---TT-T-AT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
*
10914 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-AT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * *
10963 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CC----T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* *
11012 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
11051 GCACTTTTAA
Statistics
Matches: 348, Mismatches: 42, Indels: 47
0.80 0.10 0.11
Matches are distributed among these distances:
48 2 0.01
49 164 0.47
50 2 0.01
51 2 0.01
52 43 0.12
53 2 0.01
54 8 0.02
55 70 0.20
56 1 0.00
57 1 0.00
58 1 0.00
59 1 0.00
61 5 0.01
62 5 0.01
63 2 0.01
64 5 0.01
66 1 0.00
67 33 0.09
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:10830 original size:49 final size:49
Alignment explanation
Indices: 10757--11116 Score: 435
Period size: 49 Copynumber: 7.3 Consensus size: 49
10747 TTTCTCATCA
* * * * *
10757 TCATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCT
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
* * *
10806 TCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTT
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CC----T
* * * * * *
10860 CTCATCTTTAAGCCCAATATCGTTGGCCTTGAATCACCATATTGGCACCT
1 -TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
* * *
10910 TTATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
* *
10959 TTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCT
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
11008 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
*
11054 -C-T-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
1 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
*
11100 TTATCTTTAAGTCCAAT
1 TCATCTTTAAGTCCAAT
11117 ATCGCTAGCC
Statistics
Matches: 270, Mismatches: 29, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
43 40 0.15
44 1 0.00
45 1 0.00
48 1 0.00
49 185 0.69
50 2 0.01
54 3 0.01
55 37 0.14
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (49 bp):
TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
Found at i:10876 original size:171 final size:153
Alignment explanation
Indices: 10762--11196 Score: 416
Period size: 153 Copynumber: 2.9 Consensus size: 153
10752 CATCATCATT
*
10762 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
* * *
10827 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCTTGA
66 CTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGTGA
*
10892 ATCACCATATTGGCACCTTTATC
131 ATCAACATATTGGCACCTTTATC
* * *
10915 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
* * * * * * * *
10980 CTGGCCTTGACTCAGCACATTGGCA-CC----T-TCATCTTTAAGTCCAATGTAGCTGGCCTTGA
66 CTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGTGA
* *
11039 ATCAGCACATTGGCA-C----T-
131 ATCAACATATTGGCACCTTTATC
* * * * * * * *
11056 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
* ** * * * * * *
11121 CTAGCC--GCATATTGGCTCCTT--TATCCTTTTTCTCATCTCTAAACCCAATATCGTTGGCCGT
66 CTGGCCTTG-A-ATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGT
*
11182 GAATCAACGTATTGG
129 GAATCAACATATTGG
11197 TCCTTTCATC
Statistics
Matches: 239, Mismatches: 35, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
139 2 0.01
140 3 0.01
141 71 0.30
142 1 0.00
144 1 0.00
145 34 0.14
146 1 0.00
147 40 0.17
148 1 0.00
152 2 0.01
153 83 0.35
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (153 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
CTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGTGA
ATCAACATATTGGCACCTTTATC
Found at i:10932 original size:104 final size:99
Alignment explanation
Indices: 10757--11116 Score: 448
Period size: 104 Copynumber: 3.7 Consensus size: 99
10747 TTTCTCATCA
* * *
10757 TCATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAA
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAA
*
10822 TGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTT
66 TGTAGCTGGCCTTGAATCAGCACATTGACA-CC---TT
* * * *
10860 CTCATCTTTAAGCCCAATATCGTTGGCCTTGAATCACCATATTGGCACCTTTATCTTTAAGTCCA
1 -TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCA
* * *
10925 ATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
65 ATGTAGCTGGCCTTGAATCAGCACATTGACACCTT
* * * *
10960 T-ATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAA
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAA
*
11024 TGTAGCTGGCCTTGAATCAGCACATTGGCA----
66 TGTAGCTGGCCTTGAATCAGCACATTGACACCTT
* * *
11054 -C-T-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAA
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAA
11116 T
66 T
11117 ATCGCTAGCC
Statistics
Matches: 231, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
92 58 0.25
93 1 0.00
98 83 0.36
99 1 0.00
100 2 0.01
103 2 0.01
104 84 0.36
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (99 bp):
TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAA
TGTAGCTGGCCTTGAATCAGCACATTGACACCTT
Found at i:11075 original size:43 final size:43
Alignment explanation
Indices: 11012--11102 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
11002 GCACCTTCAT
11012 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
11055 TTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
11098 CTTTA
1 CTTTA
11103 TCTTTAAGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:11150 original size:92 final size:92
Alignment explanation
Indices: 10945--11150 Score: 233
Period size: 92 Copynumber: 2.2 Consensus size: 92
10935 CCTTGAATCA
*
10945 GCATATTGGCACCTTTAT-C-TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCT
1 GCATATTGGC-CCTTTATCCTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
* *
11008 TCATCTTTAAGTCCAATGTAGCTGGCCTT
65 TCATCTTTAAGTCCAATATAGCTAGCC-T
** * * ** *
11037 G-A-ATCAGCACATTGGCACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
1 GCATATTGGCCCTTTATC-CTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
* *
11100 TTATCTTTAAGTCCAATATCGCTAGCC-
65 TCATCTTTAAGTCCAATATAGCTAGCCT
11127 GCATATTGGCTCCTTTATCCTTTT
1 GCATATTGGC-CCTTTATCCTTTT
11151 TCTCATCTCT
Statistics
Matches: 90, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
89 3 0.03
90 5 0.06
91 3 0.03
92 75 0.83
93 4 0.04
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.34
Consensus pattern (92 bp):
GCATATTGGCCCTTTATCCTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
CATCTTTAAGTCCAATATAGCTAGCCT
Found at i:11874 original size:13 final size:13
Alignment explanation
Indices: 11856--11880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11846 CATAAAATGT
11856 TGTATCGATACAA
1 TGTATCGATACAA
11869 TGTATCGATACA
1 TGTATCGATACA
11881 TGTTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11961 original size:13 final size:13
Alignment explanation
Indices: 11943--11967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11933 ATCACTTAAA
11943 TGTATCGATACAT
1 TGTATCGATACAT
11956 TGTATCGATACA
1 TGTATCGATACA
11968 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12032 original size:52 final size:52
Alignment explanation
Indices: 11976--12156 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
11966 CACTGATCTT
*
11976 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
12028 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
12080 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
12132 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
12157 TCATATTTCG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:17477 original size:6 final size:6
Alignment explanation
Indices: 17468--17492 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17458 TTTTTATTTT
17468 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
17493 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:23958 original size:17 final size:18
Alignment explanation
Indices: 23907--23971 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
23897 AATTTAAATA
23907 ATTATATTAAAAATTATT
1 ATTATATTAAAAATTATT
*
23925 ATAATATTAAAAATTATT
1 ATTATATTAAAAATTATT
* *
23943 -TTATATTAATATTTATAT
1 ATTATATTAAAAATTAT-T
*
23961 ATTTTATTAAA
1 ATTATATTAAA
23972 TAAATAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
17 13 0.33
18 18 0.46
19 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATATTAAAAATTATT
Found at i:28702 original size:74 final size:76
Alignment explanation
Indices: 28559--28705 Score: 169
Period size: 74 Copynumber: 2.0 Consensus size: 76
28549 TCATTTATTT
* *
28559 ATTATCAAATAAATTTCATTTACTCAAAATCTTTCAATACAATTAGGATTCTTATTTACAAATAC
1 ATTATCAAATAAATTTCATTTACTCAAAATCTTTCAATACAATGAGAATTCTTATTTACAAATAC
28624 AATAAATCCTA
66 AATAAATCCTA
* * *
28635 ATTATCCAATAAATTT-ATTTTA-TC-AAATCTTGT-AATATAATGAGAATT-TTGATTTATAAA
1 ATTATCAAATAAATTTCA-TTTACTCAAAATCTT-TCAATACAATGAGAATTCTT-ATTTACAAA
**
28695 TGTAATAAATC
63 TACAATAAATC
28706 TTATTAATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
73 2 0.03
74 36 0.59
75 4 0.07
76 19 0.31
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.41
Consensus pattern (76 bp):
ATTATCAAATAAATTTCATTTACTCAAAATCTTTCAATACAATGAGAATTCTTATTTACAAATAC
AATAAATCCTA
Found at i:30034 original size:16 final size:17
Alignment explanation
Indices: 30000--30034 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29990 TTCTTTTTTT
*
30000 ATTTAATTTTTAATTAA
1 ATTTAATTTTTAATAAA
30017 ATTTAATTTTT-ATAAA
1 ATTTAATTTTTAATAAA
30033 AT
1 AT
30035 AAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTAATTTTTAATAAA
Found at i:31812 original size:21 final size:21
Alignment explanation
Indices: 31786--31828 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31776 TTTTGGTGGG
31786 ATTATTTTCAAGTATATTATC
1 ATTATTTTCAAGTATATTATC
* *
31807 ATTATTTTTAGGTATATTATC
1 ATTATTTTCAAGTATATTATC
31828 A
1 A
31829 AGATGTGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTATTTTCAAGTATATTATC
Found at i:32083 original size:12 final size:13
Alignment explanation
Indices: 32054--32080 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32044 AATAAAATTT
32054 AATTTATGAATAA
1 AATTTATGAATAA
32067 AATTTATGAATAA
1 AATTTATGAATAA
32080 A
1 A
32081 TTTCACTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AATTTATGAATAA
Found at i:32190 original size:19 final size:19
Alignment explanation
Indices: 32143--32190 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
32133 AAAAAATATA
* *
32143 ATTATTTTTATTTAATTAT
1 ATTATTTTCACTTAATTAT
* *
32162 -TTAATTTCACTTAATTTT
1 ATTATTTTCACTTAATTAT
32180 ATTATTTTCAC
1 ATTATTTTCAC
32191 AAATTAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTTTCACTTAATTAT
Found at i:35158 original size:22 final size:21
Alignment explanation
Indices: 35133--35176 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
35123 TATTTTTATT
35133 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TAT-AAAATATA
35155 TAAATATTAATATAAAATATA
1 TAAATATTAATATAAAATATA
35176 T
1 T
35177 TTTTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 8 0.38
23 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:36297 original size:2 final size:2
Alignment explanation
Indices: 36290--36350 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
36280 CAATGTGCCT
36290 TA TA TA TA TA 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 TA TA
36332 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
36351 TTCCGGCATC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37623 original size:22 final size:21
Alignment explanation
Indices: 37597--37638 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
37587 GGTTTAAATT
37597 AAAATAATTTTAAATGTTAAAA
1 AAAATAATTTT-AATGTTAAAA
**
37619 AAAATTCTTTTAATGTTAAA
1 AAAATAATTTTAATGTTAAA
37639 TAAGTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAATAATTTTAATGTTAAAA
Found at i:37660 original size:20 final size:21
Alignment explanation
Indices: 37635--37677 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
37625 CTTTTAATGT
37635 TAAATAAGTAATAAAAAT-AA
1 TAAATAAGTAATAAAAATGAA
* *
37655 TAAATAATTGATAAAAATGAA
1 TAAATAAGTAATAAAAATGAA
37676 TA
1 TA
37678 TTTTTGACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (21 bp):
TAAATAAGTAATAAAAATGAA
Found at i:38197 original size:21 final size:20
Alignment explanation
Indices: 38157--38196 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38147 TTTTTTTAAA
* *
38157 AAAAATAAATGGATAGTTTT
1 AAAAATAAATGAAAAGTTTT
38177 AAAAATAAATGAAAAGTTTT
1 AAAAATAAATGAAAAGTTTT
38197 TTTTAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (20 bp):
AAAAATAAATGAAAAGTTTT
Found at i:39632 original size:7 final size:8
Alignment explanation
Indices: 39612--39642 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
39602 AAATAATATC
39612 ATTTTTTA
1 ATTTTTTA
39620 ATTTTTTA
1 ATTTTTTA
39628 ATTTTTTA
1 ATTTTTTA
39636 ATTTTTT
1 ATTTTTT
39643 TTAGTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTTTTTA
Found at i:40299 original size:2 final size:2
Alignment explanation
Indices: 40288--40319 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
40278 CCAAAGTTTA
40288 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40320 AATGTTAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41083 original size:27 final size:27
Alignment explanation
Indices: 41053--41136 Score: 72
Period size: 27 Copynumber: 3.1 Consensus size: 27
41043 TAACGATATT
41053 AATATTTTAAAATAAATTAAATAATAA
1 AATATTTTAAAATAAATTAAATAATAA
41080 AATA---TAAATATTAAATTAAAATAAATAA
1 AATATTTTAAA-A-TAAATT-AAAT-AATAA
*
41108 AA-ATTTATAAAAT-ATTTAAATAA-AA
1 AATATTT-TAAAATAAATTAAATAATAA
41133 AATA
1 AATA
41137 GTATAGTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 19
0.70 0.01 0.28
Matches are distributed among these distances:
24 4 0.09
25 5 0.11
26 9 0.19
27 13 0.28
28 10 0.21
29 1 0.02
30 1 0.02
31 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AATATTTTAAAATAAATTAAATAATAA
Found at i:41105 original size:31 final size:33
Alignment explanation
Indices: 41053--41133 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 33
41043 TAACGATATT
* *
41053 AATATTTTAAAATAAATTAAATAATAAA-ATAT-A
1 AATA-TTTAAATTAAAATAAATAA-AAATATATAA
*
41086 AATA-TTAAATTAAAATAAATAAAAATTTATAA
1 AATATTTAAATTAAAATAAATAAAAATATATAA
*
41118 AATATTTAAATAAAAA
1 AATATTTAAATTAAAA
41134 ATAGTATAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 3 0.07
31 19 0.46
32 5 0.12
33 14 0.34
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
AATATTTAAATTAAAATAAATAAAAATATATAA
Found at i:41527 original size:14 final size:13
Alignment explanation
Indices: 41499--41608 Score: 69
Period size: 13 Copynumber: 8.8 Consensus size: 13
41489 AAAATATTTT
*
41499 ATATT-TATTTTA
1 ATATTATATATTA
41511 ATATTAATATATTA
1 ATATT-ATATATTA
41525 ATATTATATA-TA
1 ATATTATATATTA
* *
41537 A-ATTTTATGTTAA
1 ATATTATATATT-A
41550 ATATT-TATATT-
1 ATATTATATATTA
41561 ATATTATAT-TT-
1 ATATTATATATTA
*
41572 TTATTAT-T-TTA
1 ATATTATATATTA
41583 TATATTATAT-TTA
1 -ATATTATATATTA
41596 TATATATATATAT
1 -ATAT-TATATAT
41609 ATGAGATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
10 3 0.04
11 19 0.23
12 18 0.22
13 21 0.26
14 19 0.23
15 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (13 bp):
ATATTATATATTA
Found at i:41532 original size:31 final size:31
Alignment explanation
Indices: 41497--41598 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
41487 TTAAAATATT
41497 TTATATT-TATTTTAATATTAATATATTAATA
1 TTATATTATATTTT-ATATTAATATATTAATA
* * *
41528 TTATATATAAATTTTATGTTAA-ATATTTATA
1 TTATAT-TATATTTTATATTAATATATTAATA
41559 TTATATTATATTTT-TATT-AT-T-TTATATA
1 TTATATTATATTTTATATTAATATATTA-ATA
41587 TTATATTTATAT
1 TTATA-TTATAT
41599 ATATATATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
27 2 0.03
28 10 0.17
29 9 0.15
30 7 0.12
31 20 0.33
32 7 0.12
33 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (31 bp):
TTATATTATATTTTATATTAATATATTAATA
Found at i:41535 original size:33 final size:33
Alignment explanation
Indices: 41491--41604 Score: 110
Period size: 33 Copynumber: 3.5 Consensus size: 33
41481 TAATATTTAA
* *
41491 AATATTTTATATTTATTTTAATATTAATATATT
1 AATATTATATATATATTTTAATATTAATATATT
* *
41524 AATATTATATATAAATTTT-ATGTTAA-ATATT
1 AATATTATATATATATTTTAATATTAATATATT
* * *
41555 TATATTATAT-TATATTTTTATTATTTTATATATT
1 AATATTATATATATA-TTTTAATA-TTAATATATT
41589 -ATATTTATATATATAT
1 AATA-TTATATATATAT
41605 ATATATGAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
30 3 0.05
31 18 0.27
32 7 0.11
33 22 0.33
34 12 0.18
35 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
AATATTATATATATATTTTAATATTAATATATT
Found at i:41595 original size:21 final size:23
Alignment explanation
Indices: 41492--41610 Score: 75
Period size: 25 Copynumber: 5.0 Consensus size: 23
41482 AATATTTAAA
41492 ATATTTTATATTTATTTTA-ATATT
1 ATATTTTATA--TATTTTATATATT
* *
41516 AATATATTA-ATATTATATATAAATT
1 -ATATTTTATATATT-T-TATATATT
* * *
41541 TTATGTTAAATATTTATATTATATT
1 ATATTTTATATATTT-TA-TATATT
41566 ATATTTT-TATTATTTTATATATT
1 ATATTTTATA-TATTTTATATATT
*
41589 ATA-TTTATATATATATATATAT
1 ATATTTTATATAT-TTTATATAT
41611 GAGATGAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
22 10 0.13
23 20 0.26
24 16 0.21
25 31 0.40
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (23 bp):
ATATTTTATATATTTTATATATT
Found at i:41598 original size:6 final size:6
Alignment explanation
Indices: 41496--41610 Score: 64
Period size: 6 Copynumber: 19.2 Consensus size: 6
41486 TTTAAAATAT
* * *
41496 TTTATA TTTAT- TTTAATA TTAATA TATTA-A TATTATA TATAAA TTT-TA
1 TTTATA TTTATA TTT-ATA TTTATA T-TTATA T-TTATA TTTATA TTTATA
*
41544 TGTTAAATA TTTATA -TTATA -TTATA TTTTTA -TTAT- TTTATA TATTATA
1 T-TT--ATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T-TTATA
* *
41592 TTTATA TATATA TATATA T
1 TTTATA TTTATA TTTATA T
41611 GAGATGAATA
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
5 22 0.25
6 49 0.56
7 12 0.14
8 2 0.02
9 3 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (6 bp):
TTTATA
Found at i:41745 original size:32 final size:32
Alignment explanation
Indices: 41709--41801 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 32
41699 ATTCAGTTTA
41709 AATTATTATTTAATAATAAAAATAATTTTTTT
1 AATTATTATTTAATAATAAAAATAATTTTTTT
* * *
41741 AATTA-AATTTAATTATAAAAATAA-TATTTT
1 AATTATTATTTAATAATAAAAATAATTTTTTT
* * * *
41771 AATAATATAATAAATAATAAAATAAAATTTT
1 AATTAT-TATTTAATAATAAAA-ATAATTTT
41802 AAGATGATCT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
30 9 0.19
31 17 0.36
32 16 0.34
33 3 0.06
34 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AATTATTATTTAATAATAAAAATAATTTTTTT
Found at i:41773 original size:20 final size:22
Alignment explanation
Indices: 41748--41789 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
41738 TTTAATTAAA
41748 TTTAAT-TATAA-AAATAATAT
1 TTTAATATATAATAAATAATAT
41768 TTTAATAATATAATAAATAATA
1 TTTAAT-ATATAATAAATAATA
41790 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
22 5 0.26
23 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAATATATAATAAATAATAT
Found at i:45999 original size:27 final size:27
Alignment explanation
Indices: 45969--46026 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
45959 TTAATTCGAA
**
45969 TTAAATTATTTTTATTTTTAAAATT-TT
1 TTAAATTATTTTTAAATTT-AAATTATT
45996 TTAAATTATTTTTAAATTTAAATTATT
1 TTAAATTATTTTTAAATTTAAATTATT
46023 TTAA
1 TTAA
46027 TTTTAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTAAATTATTTTTAAATTTAAATTATT
Found at i:46007 original size:11 final size:11
Alignment explanation
Indices: 45980--46013 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
45970 TAAATTATTT
45980 TTATTTTTAAA
1 TTATTTTTAAA
*
45991 AT-TTTTTAAA
1 TTATTTTTAAA
46001 TTATTTTTAAA
1 TTATTTTTAAA
46012 TT
1 TT
46014 TAAATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTTTAAA
Found at i:46026 original size:16 final size:16
Alignment explanation
Indices: 45995--46087 Score: 96
Period size: 16 Copynumber: 5.8 Consensus size: 16
45985 TTTAAAATTT
45995 TTTAAATTATTTTTAAA
1 TTTAAATTA-TTTTAAA
*
46012 TTTAAATTATTTTAAT
1 TTTAAATTATTTTAAA
* * *
46028 TTTAAATCACTTTAAT
1 TTTAAATTATTTTAAA
*
46044 TTTAAATTATTTCAAA
1 TTTAAATTATTTTAAA
* * *
46060 TTCAAATCATTTTAAG
1 TTTAAATTATTTTAAA
*
46076 TTAAAATTATTT
1 TTTAAATTATTT
46088 CAGATTCAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
16 54 0.86
17 9 0.14
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:46048 original size:32 final size:32
Alignment explanation
Indices: 46006--46098 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 32
45996 TTAAATTATT
* * *
46006 TTTAAATTTAAATTATTTTAATTTTAAATCAC
1 TTTAAATTTAAATTATTTCAAATTCAAATCAC
* *
46038 TTTAATTTTAAATTATTTCAAATTCAAATCAT
1 TTTAAATTTAAATTATTTCAAATTCAAATCAC
* * *
46070 TTTAAGTTAAAATTATTTCAGATTCAAAT
1 TTTAAATTTAAATTATTTCAAATTCAAAT
46099 TAATCGAGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (32 bp):
TTTAAATTTAAATTATTTCAAATTCAAATCAC
Found at i:46098 original size:16 final size:15
Alignment explanation
Indices: 46047--46100 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
46037 CTTTAATTTT
46047 AAATTATTTCAAATTC
1 AAATTATTTC-AATTC
* * *
46063 AAATCATTTTAAGTTA
1 AAATTATTTCAA-TTC
46079 AAATTATTTCAGATTC
1 AAATTATTTCA-ATTC
46095 AAATTA
1 AAATTA
46101 ATCGAGTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 27 0.90
17 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (15 bp):
AAATTATTTCAATTC
Found at i:46560 original size:13 final size:14
Alignment explanation
Indices: 46533--46561 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
46523 ATATGGATAA
46533 TAAATTTGAATATT
1 TAAATTTGAATATT
46547 TAAATTTG-ATATT
1 TAAATTTGAATATT
46560 TA
1 TA
46562 TTTACATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TAAATTTGAATATT
Found at i:46591 original size:19 final size:19
Alignment explanation
Indices: 46543--46604 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
46533 TAAATTTGAA
*
46543 TATTTAA-ATTTGATA-TT
1 TATTTAATATTTAATATTT
46560 TATTTACATATTTAAT-TTT
1 TATTTA-ATATTTAATATTT
*
46579 TATTTAATAATTTTATATTT
1 TATTTAAT-ATTTAATATTT
46599 T-TTTAA
1 TATTTAA
46605 AAAAATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 25 0.66
20 4 0.11
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTAATATTTAATATTT
Found at i:47312 original size:12 final size:12
Alignment explanation
Indices: 47297--47348 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
47287 TTTATTTTAT
47297 TATTTAAAATAA
1 TATTTAAAATAA
* *
47309 TATTAAAAATTA
1 TATTTAAAATAA
* *
47321 TTTTTATAATAA
1 TATTTAAAATAA
*
47333 TATTTAATA-AA
1 TATTTAAAATAA
47344 TATTT
1 TATTT
47349 TTTATTATTT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
11 7 0.23
12 24 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTTAAAATAA
Found at i:47339 original size:25 final size:25
Alignment explanation
Indices: 47293--47350 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
47283 AAAATTTATT
47293 TTATTATTTAAAATAATATTAA-AAA
1 TTATT-TTTAAAATAATATTAATAAA
*
47318 TTATTTTTATAATAATATTTAATAAA
1 TTATTTTTAAAATAATA-TTAATAAA
47344 -TATTTTT
1 TTATTTTT
47351 TATTATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 11 0.37
25 16 0.53
26 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTATTTTTAAAATAATATTAATAAA
Found at i:47613 original size:14 final size:14
Alignment explanation
Indices: 47594--47662 Score: 68
Period size: 14 Copynumber: 4.6 Consensus size: 14
47584 AATCTTATCG
47594 AAAATTTTAAACTT
1 AAAATTTTAAACTT
47608 AAAATTTTATATAACATT
1 AAAA-TTT-TA-AAC-TT
**
47626 AAAATTTT-ATTTT
1 AAAATTTTAAACTT
47639 ACAAATTTTAAACTT
1 A-AAATTTTAAACTT
47654 AAAATTTTA
1 AAAATTTTA
47663 TTTTAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
13 3 0.07
14 20 0.44
15 7 0.16
16 3 0.07
17 6 0.13
18 6 0.13
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (14 bp):
AAAATTTTAAACTT
Found at i:47762 original size:23 final size:24
Alignment explanation
Indices: 47722--47771 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
47712 TATTTTTTTA
*
47722 TAAATATAAAAAATA-TTTATATT
1 TAAATATAAAAAATATTTTAAATT
47745 TAAAT-TAAAAAATAATTTTAAATT
1 TAAATATAAAAAAT-ATTTTAAATT
47769 TAA
1 TAA
47772 TTTATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 8 0.33
23 6 0.25
24 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAATATAAAAAATATTTTAAATT
Found at i:48028 original size:27 final size:27
Alignment explanation
Indices: 47998--48052 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
47988 AATATTTTTA
47998 TTTTTAAATAATAATTT-AAATTTAATT
1 TTTTTAAA-AATAATTTAAAATTTAATT
*
48025 TTTTTAAAAATTATTTAAAATTTAATT
1 TTTTTAAAAATAATTTAAAATTTAATT
48052 T
1 T
48053 ATATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTTAAAAATAATTTAAAATTTAATT
Found at i:48059 original size:27 final size:27
Alignment explanation
Indices: 48002--48060 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
47992 TTTTTATTTT
* *
48002 TAAATAATAATTTAAATTTAATTTTTT
1 TAAATAATAATTTAAATTTAATTTATA
*
48029 TAAA-AATTATTTAAAATTTAATTTATA
1 TAAATAATAATTT-AAATTTAATTTATA
48056 TAAAT
1 TAAAT
48061 TAAATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAAATAATAATTTAAATTTAATTTATA
Found at i:48393 original size:6 final size:6
Alignment explanation
Indices: 48382--48411 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
48372 AGGAAAGTGA
48382 TGCATG TGCATG TGCATG TGCATG TGCATG
1 TGCATG TGCATG TGCATG TGCATG TGCATG
48412 ACATGTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
TGCATG
Found at i:48783 original size:20 final size:21
Alignment explanation
Indices: 48750--48809 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
48740 TTAAAATATT
48750 ATACAA-ATATATAAATATAA
1 ATACAACATATATAAATATAA
* * *
48770 TTATAACATA-ATAAAAATAA
1 ATACAACATATATAAATATAA
*
48790 ATACAACATATATATATATA
1 ATACAACATATATAAATATA
48810 TATATATAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 21 0.68
21 10 0.32
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.32
Consensus pattern (21 bp):
ATACAACATATATAAATATAA
Found at i:56681 original size:15 final size:15
Alignment explanation
Indices: 56661--56708 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
56651 TATTGAGAAA
*
56661 AAATTATATTAAAAT
1 AAATTATAGTAAAAT
56676 AAATTATAGTAAAAT
1 AAATTATAGTAAAAT
*
56691 AAA-TAT-GAAAAAT
1 AAATTATAGTAAAAT
56704 AAATT
1 AAATT
56709 TTGAACATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 9 0.30
14 4 0.13
15 17 0.57
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (15 bp):
AAATTATAGTAAAAT
Found at i:56969 original size:24 final size:24
Alignment explanation
Indices: 56942--57000 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
56932 ATTTAAAAAT
* *
56942 AAAATAATAAATTAT-TTTATCAA
1 AAAAAAATAAATCATATTTATCAA
* *
56965 AAAAAATTAAAACATATTTATCAA
1 AAAAAAATAAATCATATTTATCAA
*
56989 ATAAAAATAAAT
1 AAAAAAATAAAT
57001 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAAAATAAATCATATTTATCAA
Found at i:57094 original size:19 final size:19
Alignment explanation
Indices: 57070--57106 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57060 TTAATTAAGT
*
57070 TATTATTCCATTCTAATTC
1 TATTATTCCAATCTAATTC
*
57089 TATTATTGCAATCTAATT
1 TATTATTCCAATCTAATT
57107 GATTTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (19 bp):
TATTATTCCAATCTAATTC
Found at i:58239 original size:101 final size:100
Alignment explanation
Indices: 58058--58564 Score: 685
Period size: 101 Copynumber: 5.0 Consensus size: 100
58048 ACAATGAAAA
* * *
58058 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAGAAGAAAATTGGGTTTTTGGATGGGTAA
1 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAACTGGG-TTTTGGATAGGTAA
** * * *
58123 CTTCTATTACCCAATTCATTGAAATTACATTTTATT
65 CTTCTATCGCTCAATTCATTGAAGTTACATTTTGTT
* *
58159 ACCAACAAAGTATAAAAAGTATTTGATGAAAATCCTAAAAGAAAACTGGGTTTTGGATAGGTAAC
1 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAACTGGGTTTTGGATAGGTAAC
* *
58224 GTCTATAAGCTCAATTCATTGAAGTTACATTTTGTT
66 TTCTAT-CGCTCAATTCATTGAAGTTACATTTTGTT
* *
58260 ACCACC-AAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAACTGGGTTTTTGATTACGTAA
1 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAACTGGGTTTTGGA-TAGGTAA
*
58324 CTTCTATCGTTCAATTCATTGAAGTTACATTTTGTT
65 CTTCTATCGCTCAATTCATTGAAGTTACATTTTGTT
* * * * *
58360 ACCGCCAAAGTACAGAAAGTGTTTGATGAAAATCCTAAAAGAAAACTGAGTATTTGGATAAGTAA
1 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAACTGGGT-TTTGGATAGGTAA
* * *
58425 TTTCTATCGATCAGTTCATTGAAGTTACATTTTGTT
65 CTTCTATCGCTCAATTCATTGAAGTTACATTTTGTT
* * * *
58461 ACCACCAAAGCATAGAAAGTGTTTGATGAAAATCCTAAAAGAAAATTGGGTTTCTAGATAGGTAA
1 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAACTGGGTTT-TGGATAGGTAA
58526 CTTCTATCGCTCAATATTCATTAGAA-TTACATTTTGTT
65 CTTCTATCGCTC-A-ATTCATT-GAAGTTACATTTTGTT
58564 A
1 A
58565 TTATTTTTAT
Statistics
Matches: 361, Mismatches: 37, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
100 101 0.28
101 232 0.64
102 6 0.02
103 19 0.05
104 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (100 bp):
ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAACTGGGTTTTGGATAGGTAAC
TTCTATCGCTCAATTCATTGAAGTTACATTTTGTT
Found at i:58445 original size:201 final size:200
Alignment explanation
Indices: 58058--58564 Score: 703
Period size: 201 Copynumber: 2.5 Consensus size: 200
58048 ACAATGAAAA
* *
58058 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAGAAGAAAATTGGGTTTTTGGATGGGTAA
1 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAATTGGGTTTTT-GATAGGTAA
** * * *
58123 CTTCTATTACCCAATTCATTGAAATTACATTTTATTACCAACAAAGTATAAAAAGTATTTGATGA
65 CTTCTATCGCTCAATTCATTG-AATTACATTTTGTTACCAACAAAGTACAAAAAGTATTTGATGA
* * *
58188 AAATCCTAAAAGAAAACTGGGTTTTGGATAGGTAACGTCTATAAGCTCAATTCATTGAAGTTACA
129 AAATCCTAAAAGAAAACTGAGTTTTGGATAAGTAACGTCTATAAGATCAATTCATTGAAGTTACA
58253 TTTTGTT
194 TTTTGTT
* *
58260 ACCACC-AAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAACTGGGTTTTTGATTACGTAA
1 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAATTGGGTTTTTGA-TAGGTAA
* ** * *
58324 CTTCTATCGTTCAATTCATTGAAGTTACATTTTGTTACCGCCAAAGTACAGAAAGTGTTTGATGA
65 CTTCTATCGCTCAATTCATTGAA-TTACATTTTGTTACCAACAAAGTACAAAAAGTATTTGATGA
** * *
58389 AAATCCTAAAAGAAAACTGAGTATTTGGATAAGTAATTTCTAT-CGATCAGTTCATTGAAGTTAC
129 AAATCCTAAAAGAAAACTGAGT-TTTGGATAAGTAACGTCTATAAGATCAATTCATTGAAGTTAC
58453 ATTTTGTT
193 ATTTTGTT
* * *
58461 ACCACCAAAGCATAGAAAGTGTTTGATGAAAATCCTAAAAGAAAATTGGGTTTCTAGATAGGTAA
1 ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAATTGGGTTT-TTGATAGGTAA
58526 CTTCTATCGCTCAATATTCATTAGAATTACATTTTGTTA
65 CTTCTATCGCTC-A-ATTCATT-GAATTACATTTTGTTA
58565 TTATTTTTAT
Statistics
Matches: 270, Mismatches: 27, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
200 4 0.01
201 156 0.58
202 83 0.31
203 4 0.01
204 20 0.07
205 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (200 bp):
ACCACCAAAGTATAGAAAGTATTTGATGAAAATCCTAAAAGAAAATTGGGTTTTTGATAGGTAAC
TTCTATCGCTCAATTCATTGAATTACATTTTGTTACCAACAAAGTACAAAAAGTATTTGATGAAA
ATCCTAAAAGAAAACTGAGTTTTGGATAAGTAACGTCTATAAGATCAATTCATTGAAGTTACATT
TTGTT
Found at i:58841 original size:4 final size:4
Alignment explanation
Indices: 58832--58862 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
58822 TTATTACTAT
58832 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
58863 TGACTATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:59409 original size:15 final size:15
Alignment explanation
Indices: 59373--59420 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
59363 AGGGTTCAAA
59373 ATTTT-ATTTATTAT
1 ATTTTAATTTATTAT
* *
59387 ACTATAATTTATTAT
1 ATTTTAATTTATTAT
*
59402 ATTTTAATTATATTTT
1 ATTTTAATT-TATTAT
59418 ATT
1 ATT
59421 ATGTGTGCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 3 0.11
15 16 0.59
16 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTAATTTATTAT
Found at i:59413 original size:11 final size:10
Alignment explanation
Indices: 59373--59422 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
59363 AGGGTTCAAA
59373 ATTTTATT-T
1 ATTTTATTAT
* *
59382 ATTATACTAT
1 ATTTTATTAT
*
59392 AATTTATTAT
1 ATTTTATTAT
59402 ATTTTAATTAT
1 ATTTT-ATTAT
59413 ATTTTATTAT
1 ATTTTATTAT
59423 GTGTGCATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 6 0.18
10 17 0.52
11 10 0.30
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTATTAT
Found at i:59418 original size:21 final size:20
Alignment explanation
Indices: 59373--59422 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
59363 AGGGTTCAAA
59373 ATTTTATT-TATTATACTAT
1 ATTTTATTATATTATACTAT
* * *
59392 AATTTATTATATTTTAATTAT
1 ATTTTATTATATTAT-ACTAT
59413 ATTTTATTAT
1 ATTTTATTAT
59423 GTGTGCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 7 0.28
20 5 0.20
21 13 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTATTATATTATACTAT
Found at i:59745 original size:2 final size:2
Alignment explanation
Indices: 59738--59764 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59728 TATGATTTAT
59738 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 T
59765 CTTAATTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60326 original size:36 final size:36
Alignment explanation
Indices: 60210--60327 Score: 138
Period size: 36 Copynumber: 3.3 Consensus size: 36
60200 AATTTGTAAT
60210 TATTAACAA-TATATTTATATTAAATAATAAAATATA
1 TATTAA-AATTATATTTATATTAAATAATAAAATATA
* *
60246 -AATAAAATTATATTTATGTTGAAAATAATTAAAAT-T-
1 TATTAAAATTATATTTATATT--AAATAA-TAAAATATA
*
60282 TAGT-AAATTATATTTATATTAAATAATAAAATATA
1 TATTAAAATTATATTTATATTAAATAATAAAATATA
60317 TATTAAAATTA
1 TATTAAAATTA
60328 AAAATTACAC
Statistics
Matches: 69, Mismatches: 5, Indels: 16
0.77 0.06 0.18
Matches are distributed among these distances:
33 6 0.09
34 9 0.13
35 18 0.26
36 21 0.30
37 9 0.13
38 6 0.09
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (36 bp):
TATTAAAATTATATTTATATTAAATAATAAAATATA
Found at i:61282 original size:187 final size:186
Alignment explanation
Indices: 60998--61363 Score: 592
Period size: 187 Copynumber: 2.0 Consensus size: 186
60988 GAATAATAGA
* *
60998 AAAAGATATATTTTACATATAAATTTGTTAATTTAAATATATTTATTTATTTATGACATGTTAAA
1 AAAAGATATATTTTACATATAAACTTGTTAATTTAAATATATTTATTCATTTATGACATGTTAAA
* * * *
61063 TTATCGTATTTTAAATAGATAGATGTGACACGATTAATTACTCATGTCTAAACTGTGTCTTATGC
66 TTATCGTATTTTAAATAGATAGAAGCGACACGATTAATTAATCATATCTAAACTGTGTCTTATGC
61128 TTGTTATGCATG-TTTCACACGTTTATGATATGACACGATTATGACACGAATAACAAG
131 TTGTTATGCATGCTTT-ACACGTTTATGATATGA-ACGATTATGACACGAATAACAAG
* * *
61185 AAAAGATGTATTTTACATATAAACTTGTTAATTTAAATGTGTTTATTCATTTATGACATGTTAAA
1 AAAAGATATATTTTACATATAAACTTGTTAATTTAAATATATTTATTCATTTATGACATGTTAAA
*
61250 TTATCGTATTTTAAAT-GTATAGAAGCGACACGATTAATTAATCATATCTTAACTGTGTCTTATG
66 TTATCGTATTTTAAATAG-ATAGAAGCGACACGATTAATTAATCATATCTAAACTGTGTCTTATG
*
61314 CTTGTTATGCGTGCTTTACACGTTTATGATATGAACGATTATGACACGAA
130 CTTGTTATGCATGCTTTACACGTTTATGATATGAACGATTATGACACGAA
61364 ACACGATTAC
Statistics
Matches: 166, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
186 17 0.10
187 146 0.88
188 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (186 bp):
AAAAGATATATTTTACATATAAACTTGTTAATTTAAATATATTTATTCATTTATGACATGTTAAA
TTATCGTATTTTAAATAGATAGAAGCGACACGATTAATTAATCATATCTAAACTGTGTCTTATGC
TTGTTATGCATGCTTTACACGTTTATGATATGAACGATTATGACACGAATAACAAG
Found at i:61998 original size:13 final size:13
Alignment explanation
Indices: 61980--62005 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61970 TACACCAAGT
61980 ATGTATCGATACA
1 ATGTATCGATACA
61993 ATGTATCGATACA
1 ATGTATCGATACA
62006 TAAAAAAATT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:62878 original size:18 final size:19
Alignment explanation
Indices: 62857--62899 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
62847 TTAAATATTT
62857 ATTTTTATTA-AAAAATTA
1 ATTTTTATTAGAAAAATTA
*
62875 A-TTTTATTAGAAAACTTA
1 ATTTTTATTAGAAAAATTA
*
62893 CTTTTTA
1 ATTTTTA
62900 CATGAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTTTATTAGAAAAATTA
Found at i:65678 original size:16 final size:16
Alignment explanation
Indices: 65633--65699 Score: 68
Period size: 15 Copynumber: 4.3 Consensus size: 16
65623 TAAATTTAAT
* *
65633 TAATTTAATTTTAAAA
1 TAATTTAAATATAAAA
* *
65649 TAAATAAAAT-TAAAA
1 TAATTTAAATATAAAA
65664 TAATTTAAATATAAAA
1 TAATTTAAATATAAAA
65680 -AATTTAAA-ATAAAAA
1 TAATTTAAATAT-AAAA
65695 TAATT
1 TAATT
65700 CATTTAACTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.05
15 25 0.58
16 16 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATTTAAATATAAAA
Found at i:65679 original size:31 final size:31
Alignment explanation
Indices: 65624--65699 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
65614 TTTAAATGTT
* * * *
65624 AAATTTAATTAATTTAATTTTAAAATAA-ATA
1 AAATTAAAATAATTTAAATATAAAA-AATATA
*
65655 AAATTAAAATAATTTAAATATAAAAAATTTA
1 AAATTAAAATAATTTAAATATAAAAAATATA
*
65686 AAATAAAAATAATT
1 AAATTAAAATAATT
65700 CATTTAACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATTAAAATAATTTAAATATAAAAAATATA
Found at i:65686 original size:25 final size:25
Alignment explanation
Indices: 65642--65691 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
65632 TTAATTTAAT
65642 TTTAAAATAAATAAAATTAAAATAA
1 TTTAAAATAAATAAAATTAAAATAA
*
65667 TTTAAATATAAA-AAATTTAAAATAA
1 TTTAAA-ATAAATAAAATTAAAATAA
65692 AAATAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
TTTAAAATAAATAAAATTAAAATAA
Found at i:66462 original size:15 final size:17
Alignment explanation
Indices: 66439--66476 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
66429 TTTTTTAAAA
*
66439 AATATATATTTA-TTTT
1 AATATATATTAATTTTT
66455 AATA-ATATTAATTTTT
1 AATATATATTAATTTTT
66471 AATATA
1 AATATA
66477 AAATTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 12 0.63
17 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATATATTAATTTTT
Found at i:66468 original size:19 final size:18
Alignment explanation
Indices: 66424--66470 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
66414 TATTATATAA
66424 ATAATTTTTTTAAAAAAT
1 ATAATTTTTTTAAAAAAT
*
66442 ATATATTTATTTT-AATAAT
1 ATA-ATTT-TTTTAAAAAAT
66461 ATTAATTTTT
1 A-TAATTTTT
66471 AATATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.20
19 14 0.56
20 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAATTTTTTTAAAAAAT
Found at i:66496 original size:30 final size:33
Alignment explanation
Indices: 66455--66524 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 33
66445 TATTTATTTT
*
66455 AATAATATTAATT-TTTAATATAAA-A-TTAAAA
1 AATAATATTAATTATTT-ATAAAAATATTTAAAA
66486 AATAAT-TTAATTATTTATAAAAATATTTAAAA
1 AATAATATTAATTATTTATAAAAATATTTAAAA
66518 AATAATA
1 AATAATA
66525 AAAGATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 12 0.35
31 10 0.29
32 12 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
AATAATATTAATTATTTATAAAAATATTTAAAA
Found at i:66821 original size:24 final size:25
Alignment explanation
Indices: 66768--66821 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
66758 ATTAATTAAG
* *
66768 TAAATTAAATTTTAATTTTTTATCA
1 TAAATTAAATTTTAAATATTTATCA
*
66793 T-AATTATATTTTAAATATTTA-CA
1 TAAATTAAATTTTAAATATTTATCA
66816 TAAATT
1 TAAATT
66822 TTGATACTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 3 0.12
24 21 0.84
25 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
TAAATTAAATTTTAAATATTTATCA
Found at i:67398 original size:16 final size:15
Alignment explanation
Indices: 67364--67412 Score: 64
Period size: 16 Copynumber: 3.3 Consensus size: 15
67354 TTATTTTTAT
67364 ATTATTAAATAAAAA
1 ATTATTAAATAAAAA
* *
67379 ATTATTATATTAATAA
1 ATTATTA-AATAAAAA
67395 ATTATT-AATAAAAA
1 ATTATTAAATAAAAA
67409 ATTA
1 ATTA
67413 AAATATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 10 0.34
15 7 0.24
16 12 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTATTAAATAAAAA
Found at i:67407 original size:30 final size:31
Alignment explanation
Indices: 67364--67421 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
67354 TTATTTTTAT
**
67364 ATTATTAAATAAAAAATTATTATATTAATAA
1 ATTATTAAATAAAAAATTAAAATATTAATAA
67395 ATTATT-AATAAAAAATTAAAATATTAA
1 ATTATTAAATAAAAAATTAAAATATTAA
67422 ATAATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTATTAAATAAAAAATTAAAATATTAATAA
Found at i:71279 original size:19 final size:20
Alignment explanation
Indices: 71242--71288 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
71232 GTTAATTATG
*
71242 TAATTTTTTATTAAAATAA-
1 TAATTTTTTAATAAAATAAT
**
71261 TAATTTTTTAATATTATAAT
1 TAATTTTTTAATAAAATAAT
71281 TAATTTTT
1 TAATTTTT
71289 AAAATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATTTTTTAATAAAATAAT
Found at i:71297 original size:16 final size:17
Alignment explanation
Indices: 71247--71297 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
71237 TTATGTAATT
71247 TTTTATTAAAATAA-TAA
1 TTTT-TTAAAATAATTAA
71264 TTTTTTAATATTATAATTAA
1 TTTTTTAA-A--ATAATTAA
71284 -TTTTTAAAATAATT
1 TTTTTTAAAATAATT
71298 TTTTAGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 10 0.33
17 5 0.17
18 1 0.03
19 11 0.37
20 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTTAAAATAATTAA
Found at i:71511 original size:26 final size:25
Alignment explanation
Indices: 71482--71544 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
71472 TTTAAAAATT
71482 TTAAAAATAAAAAATTAATGATTTAA
1 TTAAAAATAAAAAA-TAATGATTTAA
* * **
71508 TTAAATATATATAAATAATTTTTTAA
1 TTAAAAATA-AAAAATAATGATTTAA
71534 TTAAATAATAA
1 TTAAA-AATAA
71545 TTAAAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
TTAAAAATAAAAAATAATGATTTAA
Found at i:71549 original size:27 final size:26
Alignment explanation
Indices: 71503--71556 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
71493 AAATTAATGA
*
71503 TTTAATTAAATATATATAAATAATTT
1 TTTAATTAAATATATATAAAAAATTT
71529 TTTAATTAAATA-ATAATTAAAAAATTT
1 TTTAATTAAATATAT-A-TAAAAAATTT
71556 T
1 T
71557 AAAAATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 13 0.52
27 10 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTAATTAAATATATATAAAAAATTT
Found at i:71869 original size:19 final size:20
Alignment explanation
Indices: 71842--71880 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
71832 ATAAAATTTA
*
71842 TAATAAAAATATAAA-AAAT
1 TAATAAAAAAATAAATAAAT
*
71861 TAATTAAAAAATAAATAAAT
1 TAATAAAAAAATAAATAAAT
71881 ATGGTTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
TAATAAAAAAATAAATAAAT
Found at i:72027 original size:6 final size:6
Alignment explanation
Indices: 72016--72051 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
72006 TTATAAAAAT
*
72016 ATATAA ATATAA ATATAA ATATTA ATATATA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATA-A ATATA
72052 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:72181 original size:126 final size:124
Alignment explanation
Indices: 72028--72377 Score: 450
Period size: 121 Copynumber: 2.8 Consensus size: 124
72018 ATAAATATAA
* *
72028 ATATAAATATTAATATATAAT-ATATTTTTATTTTTTATT-TTTATATGAATAATAATTTAAGTT
1 ATATAAATATTAATATAAAATAATATTTTAATTTTTTATTATTTATATGAATAATAATTTAA-TT
* *
72091 TTTAAGTTGGGTTCGATTAAAATTTGAACACAAAAATTTTCATTAAATCTAATAATA-AAAAT
65 TTTAAGTTGGGTTCGATTCAAATTTGAA-ACAAAAATTTTAATTAAAT-TAA-AATATAAAAT
*
72153 ATATAAATATTAATATAAAATAATATTTTAATTTTTTATTAATT-TATGAATAATAATTTGAATT
1 ATATAAATATTAATATAAAATAATATTTTAATTTTTTATTATTTATATGAATAATAATTT-AATT
* * * *
72217 TTCAAGATGGGTTCGATTCAAATTTG-AA-TAAAA-TTTAATTAAATTAAATTATAAAAT
65 TTTAAGTTGGGTTCGATTCAAATTTGAAACAAAAATTTTAATTAAATTAAAATATAAAAT
*
72274 ATATAACTATTAATATAAAATAATATTTTAATTTTTTATTAATTTATA-G-ATAATAATTTAAAT
1 ATATAAATATTAATATAAAATAATATTTTAATTTTTTATT-ATTTATATGAATAATAATTT-AAT
* * *
72337 TTTTAAATTGGGTTCAATTCAAATTT-AAACAAAAATATTAA
64 TTTTAAGTTGGGTTCGATTCAAATTTGAAACAAAAATTTTAA
72378 AATTTTTAAA
Statistics
Matches: 198, Mismatches: 18, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
120 3 0.02
121 84 0.42
122 18 0.09
123 10 0.05
124 1 0.01
125 21 0.11
126 57 0.29
127 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (124 bp):
ATATAAATATTAATATAAAATAATATTTTAATTTTTTATTATTTATATGAATAATAATTTAATTT
TTAAGTTGGGTTCGATTCAAATTTGAAACAAAAATTTTAATTAAATTAAAATATAAAAT
Found at i:72314 original size:121 final size:119
Alignment explanation
Indices: 71988--72362 Score: 431
Period size: 121 Copynumber: 3.1 Consensus size: 119
71978 TTTAATAATA
* *
71988 AAATTTTAAAAAATTTAATTATAA--AAATATATAAATATAAATATAAATATTAATATATAAT-A
1 AAATTTGAAAAAATTTAATTA-AATTAAAT-TATAAA-AT--ATATAAATATTAATATAAAATAA
* * * *
72050 TATTTTTATTTTTTATT-TTTATATGAATAATAATTTAAGTTTTTAAGTTGGGTTCGATTA
61 TATTTTAATTTTTTATTAATT-TATGAATAATAATTTAA-TTTTTAAGATGGGTTCGATTC
* *
72110 AAATTTGAACACAAAAATTTTCATTAAATCT-AATAATAAAAATATATAAATATTAATATAAAAT
1 AAATTTG---A-AAAAA-TTTAATTAAAT-TAAATTAT-AAAATATATAAATATTAATATAAAAT
*
72174 AATATTTTAATTTTTTATTAATTTATGAATAATAATTTGAATTTTCAAGATGGGTTCGATTC
59 AATATTTTAATTTTTTATTAATTTATGAATAATAATTT-AATTTTTAAGATGGGTTCGATTC
*
72236 AAATTTGAATAAAATTTAATTAAATTAAATTATAAAATATATAACTATTAATATAAAATAATATT
1 AAATTTGAA-AAAATTTAATTAAATTAAATTATAAAATATATAAATATTAATATAAAATAATATT
*
72301 TTAATTTTTTATTAATTTAT-AGATAATAATTTAAATTTTTAA-ATTGGGTTCAATTC
65 TTAATTTTTTATTAATTTATGA-ATAATAATTT-AATTTTTAAGA-TGGGTTCGATTC
72357 AAATTT
1 AAATTT
72363 AAACAAAAAT
Statistics
Matches: 222, Mismatches: 15, Indels: 33
0.82 0.06 0.12
Matches are distributed among these distances:
120 2 0.01
121 87 0.39
122 22 0.10
123 5 0.02
125 21 0.09
126 64 0.29
127 15 0.07
128 6 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (119 bp):
AAATTTGAAAAAATTTAATTAAATTAAATTATAAAATATATAAATATTAATATAAAATAATATTT
TAATTTTTTATTAATTTATGAATAATAATTTAATTTTTAAGATGGGTTCGATTC
Found at i:72780 original size:12 final size:13
Alignment explanation
Indices: 72756--72780 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72746 TCACTAGGTA
72756 AAGTTATTTTTTT
1 AAGTTATTTTTTT
72769 AAGTTATTTTTT
1 AAGTTATTTTTT
72781 CAGTCTAAGG
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
AAGTTATTTTTTT
Found at i:73157 original size:2 final size:2
Alignment explanation
Indices: 73150--73189 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
73140 TCAAAGACAA
* *
73150 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73190 TTAAAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:73502 original size:14 final size:15
Alignment explanation
Indices: 73485--73521 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
73475 TTAAAATACA
*
73485 AATAAAAAT-ATATT
1 AATAAAAATAATAAT
73499 AAT-AAAATAATAAT
1 AATAAAAATAATAAT
73513 AATAAAAAT
1 AATAAAAAT
73522 TTAATTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAAAATAATAAT
Found at i:73525 original size:25 final size:25
Alignment explanation
Indices: 73476--73526 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
73466 ATACATAAAT
*
73476 TAAAATACAAATAAAAATATATTAA
1 TAAAATACAAATAAAAAAATATTAA
73501 TAAAATA-ATAATAATAAAAAT-TTAA
1 TAAAATACA-AATAA-AAAAATATTAA
73526 T
1 T
73527 TTGAAGGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 1 0.04
25 17 0.74
26 5 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
TAAAATACAAATAAAAAAATATTAA
Found at i:73526 original size:14 final size:14
Alignment explanation
Indices: 73485--73526 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
73475 TTAAAATACA
*
73485 AATAAAAATATATT
1 AATAAAAATATAAT
73499 AAT-AAAATAATAAT
1 AATAAAAAT-ATAAT
*
73513 AATAAAAATTTAAT
1 AATAAAAATATAAT
73527 TTGAAGGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.21
14 14 0.58
15 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAAAATATAAT
Found at i:73792 original size:38 final size:38
Alignment explanation
Indices: 73724--73796 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
73714 CAATAGAAAG
* *
73724 AAAAAAAAAGAAAATAAAATAAAATAAGAGAAAAAGGA
1 AAAAAAAAAGAAAACAAAAGAAAATAAGAGAAAAAGGA
*
73762 AAAAAAAAAGAAATACAAAAGAAAA-GAGAGAAAAA
1 AAAAAAAAAGAAA-ACAAAAGAAAATAAGAGAAAAA
73797 TTATGTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 22 0.71
39 9 0.29
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.05
Consensus pattern (38 bp):
AAAAAAAAAGAAAACAAAAGAAAATAAGAGAAAAAGGA
Found at i:73823 original size:10 final size:10
Alignment explanation
Indices: 73808--73868 Score: 53
Period size: 9 Copynumber: 6.6 Consensus size: 10
73798 TATGTGTTTG
73808 TATTTATATA
1 TATTTATATA
73818 TATTTATAT-
1 TATTTATATA
*
73827 TATTT-TTTA
1 TATTTATATA
*
73836 TTTTTA-ATA
1 TATTTATATA
73845 TA-TTATA-A
1 TATTTATATA
73853 -ATTTATATAA
1 TATTTATAT-A
73863 TATTTA
1 TATTTA
73869 AAATATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
7 1 0.03
8 11 0.28
9 13 0.32
10 10 0.25
11 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTTATATA
Found at i:73872 original size:18 final size:20
Alignment explanation
Indices: 73840--73878 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
73830 TTTTTATTTT
*
73840 TAATATATTATAAATTTATA
1 TAATATATTATAAATATATA
73860 TAATAT-TTA-AAATATATA
1 TAATATATTATAAATATATA
73878 T
1 T
73879 TATTTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATATTATAAATATATA
Found at i:74297 original size:31 final size:32
Alignment explanation
Indices: 74247--74332 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 32
74237 AGTATTATAA
* * *
74247 ATTCATATATATATATATTTATACACATTAAT-T
1 ATTCGTAT-TATATTTATTTA-AAACATTAATGT
*
74280 ATTCGT-TTATATTTATTTAAAACGTTAATGT
1 ATTCGTATTATATTTATTTAAAACATTAATGT
*
74311 ATTCGTATCATATTTATATTAA
1 ATTCGTATTATATTTAT-TTAA
74333 TTTTTATGCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 8 0.18
31 18 0.40
32 10 0.22
33 9 0.20
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (32 bp):
ATTCGTATTATATTTATTTAAAACATTAATGT
Found at i:75992 original size:24 final size:24
Alignment explanation
Indices: 75948--75996 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
75938 ACTTTCGTGC
* *
75948 AAGTTATAAATCTTTAATTTTATT
1 AAGTTATAAATATTAAATTTTATT
75972 AAGTTATAAA-ATTAAACTTTTATT
1 AAGTTATAAATATTAAA-TTTTATT
75996 A
1 A
75997 TTAATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
AAGTTATAAATATTAAATTTTATT
Found at i:79118 original size:17 final size:17
Alignment explanation
Indices: 79098--79141 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
79088 TTTAAAGAAC
*
79098 ATATAATATTAGTATAT
1 ATATAATATTAATATAT
* *
79115 ATATGATTTTAATATAT
1 ATATAATATTAATATAT
79132 ATATATATAT
1 ATATA-ATAT
79142 CTATATGTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
ATATAATATTAATATAT
Found at i:79932 original size:8 final size:8
Alignment explanation
Indices: 79919--79946 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
79909 ATTTTCCTTA
79919 TTTTTTTC
1 TTTTTTTC
79927 TTTTTTTC
1 TTTTTTTC
79935 TTTTTTTC
1 TTTTTTTC
79943 TTTT
1 TTTT
79947 CCGTTATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTC
Found at i:80728 original size:6 final size:6
Alignment explanation
Indices: 80719--80748 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
80709 TAACTGAAAA
*
80719 AAATTT AAATTT AAATTT AAATTT ATATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT
80749 GATCTAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:80878 original size:18 final size:20
Alignment explanation
Indices: 80841--80897 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
80831 TATTATTAAA
*
80841 TTTAAATAAAAATATATTAT
1 TTTAAATTAAAATATATTAT
80861 TTT-AATTAAAAT-TATTAT
1 TTTAAATTAAAATATATTAT
*
80879 TTTAAATTAAAATAAATTA
1 TTTAAATTAAAATATATTA
80898 ATAATCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.27
19 17 0.52
20 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATTAAAATATATTAT
Found at i:84140 original size:24 final size:25
Alignment explanation
Indices: 84094--84140 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
84084 GAATTACTGT
* * *
84094 TGGAAAAAGGTTTGGTTAGAAAGGC
1 TGGAAAAAGGTGTGCTTAAAAAGGC
84119 TGGAAAAA-GTGTGCTTAAAAAG
1 TGGAAAAAGGTGTGCTTAAAAAG
84141 CTTTGTTGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.23
Consensus pattern (25 bp):
TGGAAAAAGGTGTGCTTAAAAAGGC
Found at i:88658 original size:29 final size:28
Alignment explanation
Indices: 88576--88659 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
88566 ACTATATGGC
* * *
88576 CTTAAAATGATGAAATTTTTTAAAATGAT
1 CTTAAAATTATGAAAATTTCT-AAATGAT
* **
88605 CTT-AAATTATGTAAATAGCTTAAATGAT
1 CTTAAAATTATGAAAATTTC-TAAATGAT
88633 CTTAAAATATATGAAAATTTCTAAATG
1 CTTAAAAT-TATGAAAATTTCTAAATG
88660 CCTTTGGATT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 20 0.47
29 14 0.33
30 9 0.21
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (28 bp):
CTTAAAATTATGAAAATTTCTAAATGAT
Found at i:89269 original size:20 final size:20
Alignment explanation
Indices: 89241--89315 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
89231 TCATACCCTG
89241 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
89261 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
89281 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
89301 ATGTATCGATACATT
1 ATGTATCGATACATT
89316 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:89308 original size:40 final size:39
Alignment explanation
Indices: 89241--89318 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
89231 TCATACCCTG
* *
89241 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
89281 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
89319 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Done.