Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011314.1 Corchorus capsularis cultivar CVL-1 contig11335, whole genome shotgun sequence
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: 174694
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3014 original size:19 final size:19
Alignment explanation
Indices: 2990--3028 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2980 GAACCCCTTT
2990 TCTCCTATTGTAAAATCCA
1 TCTCCTATTGTAAAATCCA
3009 TCTCCTATTGTAAAATCCA
1 TCTCCTATTGTAAAATCCA
3028 T
1 T
3029 GCTGCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (19 bp):
TCTCCTATTGTAAAATCCA
Found at i:3598 original size:20 final size:20
Alignment explanation
Indices: 3573--3611 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3563 AAAAAGAGCA
3573 CCAATTTGCAAATCAAATGT
1 CCAATTTGCAAATCAAATGT
*
3593 CCAATTTGTAAATCAAATG
1 CCAATTTGCAAATCAAATG
3612 CCTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
CCAATTTGCAAATCAAATGT
Found at i:23903 original size:22 final size:22
Alignment explanation
Indices: 23877--23922 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
23867 TATTTTGGAG
23877 TTGTTTTTATGAAGATTTTAAT
1 TTGTTTTTATGAAGATTTTAAT
23899 TTGTTTTTATGAAGATTTTAAT
1 TTGTTTTTATGAAGATTTTAAT
23921 TT
1 TT
23923 AGTATGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (22 bp):
TTGTTTTTATGAAGATTTTAAT
Found at i:29130 original size:47 final size:47
Alignment explanation
Indices: 29014--29582 Score: 467
Period size: 47 Copynumber: 12.3 Consensus size: 47
29004 TCTTGCAAAT
* * * * * *
29014 TCGCATGGAAACGAGAAAAAACCAACTTTGGTCA-AAGAGATTGCAAAC
1 TCGCGTGGAAGCGAGAGAAGACCAACTTTGGTCACTA-A-ATTGCAGAC
* *
29062 TCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAAATTGCAGAT
1 TCGCGTGGAAGCGAGAGAAGACCAACTTTGGTCACTAAATTGCAGAC
* * * * ** *
29109 TCCCATGGAAGCAAGAGAAGACCAACTTTGGTCACTAGATTAAAGGC
1 TCGCGTGGAAGCGAGAGAAGACCAACTTTGGTCACTAAATTGCAGAC
* * *
29156 TCGCATGGAAGCGAGAAAAAGACCAACTTTGGTCACTAAATTGTAGAC
1 TCGCGTGGAAGCGAG-AGAAGACCAACTTTGGTCACTAAATTGCAGAC
* * * * *
29204 TAGCGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAGATTGTAGAA
1 TCGCGTGGAAGCGAGAGAAGACCAACTTTGGTCACTAAATTGCAGAC
* *
29251 TCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAAATTGCAGAC
1 TCGCGTGGAAGCGAGAGAAGACCAACTTTGGTCACTAAATTGCAGAC
* * * *
29298 TCACATGGAAGTGAG-GAAATACCAACTTTGG-CAC-----T-C--A-
1 TCGCGTGGAAGCGAGAG-AAGACCAACTTTGGTCACTAAATTGCAGAC
* * * *
29335 ---CATGGAAGTGAGGA-AATACCAACTTTGGCCACTAAATTGCAGAC
1 TCGCGTGGAAGCGA-GAGAAGACCAACTTTGGTCACTAAATTGCAGAC
* * * * * *
29379 TCACGTGGAAGTGAG-GAAAGACCAACTTTGGCCACCAAATTGTAGAA
1 TCGCGTGGAAGCGAGAG-AAGACCAACTTTGGTCACTAAATTGCAGAC
*
29426 TCGCGTGGAAGCGAG-GAAAGACCAACTTTGGTCACTAAATTGCAGAA
1 TCGCGTGGAAGCGAGAG-AAGACCAACTTTGGTCACTAAATTGCAGAC
29473 TCGCGTGGAAGCGAG-GAAAGACCAACTTTGGTCACTAAATTGCAGAC
1 TCGCGTGGAAGCGAGAG-AAGACCAACTTTGGTCACTAAATTGCAGAC
** * * * * * *
29520 TCATGTGGAAGTGAGAAAAGGCCAACTTTGGCCACTACAA-CGTAGAC
1 TCGCGTGGAAGCGAGAGAAGACCAACTTTGGTCACTA-AATTGCAGAC
* *
29567 TCGCATGGAAGTGAGA
1 TCGCGTGGAAGCGAGA
29583 ATAGATTACC
Statistics
Matches: 442, Mismatches: 57, Indels: 45
0.81 0.10 0.08
Matches are distributed among these distances:
34 25 0.06
35 4 0.01
38 1 0.00
40 2 0.00
41 2 0.00
43 1 0.00
46 4 0.01
47 328 0.74
48 74 0.17
49 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (47 bp):
TCGCGTGGAAGCGAGAGAAGACCAACTTTGGTCACTAAATTGCAGAC
Found at i:29322 original size:94 final size:94
Alignment explanation
Indices: 29034--29581 Score: 536
Period size: 94 Copynumber: 5.9 Consensus size: 94
29024 ACGAGAAAAA
** *
29034 ACCAACTTTGGTCAAAGAGATTGCA-AACTCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCACT
1 ACCAACTTTGGTC-ACTAGATTGCAGAA-TCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACT
* * * *
29098 AAATTGCAGATTCCCATGGAAG-CAAGAGAAG
64 AAATTGCAGACTCACATGGAAGTGAGGA-AAG
** ** * *
29129 ACCAACTTTGGTCACTAGATTAAAGGCTCGCATGGAAGCGAGAAAAAGACCAACTTTGGTCACTA
1 ACCAACTTTGGTCACTAGATTGCAGAATCACGTGGAAGCGAG-AAAAGACCAACTTTGGTCACTA
* * * *
29194 AATTGTAGACT-AGCGTGGAAGCGAGAAAAG
65 AATTGCAGACTCA-CATGGAAGTGAGGAAAG
*
29224 ACCAACTTTGGTCACTAGATTGTAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAA
1 ACCAACTTTGGTCACTAGATTGCAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAA
*
29289 ATTGCAGACTCACATGGAAGTGAGGAAAT
66 ATTGCAGACTCACATGGAAGTGAGGAAAG
* * * *
29318 ACCAACTTTGG-CAC-----T-C---A-CA--TGGAAGTGAGGAAATACCAACTTTGGCCACTAA
1 ACCAACTTTGGTCACTAGATTGCAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAA
*
29370 ATTGCAGACTCACGTGGAAGTGAGGAAAG
66 ATTGCAGACTCACATGGAAGTGAGGAAAG
* * * * * *
29399 ACCAACTTTGGCCACCAAATTGTAGAATCGCGTGGAAGCGAGGAAAGACCAACTTTGGTCACTAA
1 ACCAACTTTGGTCACTAGATTGCAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAA
* * * *
29464 ATTGCAGAATCGCGTGGAAGCGAGGAAAG
66 ATTGCAGACTCACATGGAAGTGAGGAAAG
* * * * * *
29493 ACCAACTTTGGTCACTAAATTGCAGACTCATGTGGAAGTGAGAAAAGGCCAACTTTGGCCACTAC
1 ACCAACTTTGGTCACTAGATTGCAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTA-
* * *
29558 AA-CGTAGACTCGCATGGAAGTGAG
65 AATTGCAGACTCACATGGAAGTGAG
29582 AATAGATTAC
Statistics
Matches: 379, Mismatches: 55, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
81 67 0.18
82 3 0.01
83 2 0.01
84 1 0.00
87 1 0.00
88 1 0.00
91 1 0.00
92 1 0.00
93 3 0.01
94 204 0.54
95 93 0.25
96 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (94 bp):
ACCAACTTTGGTCACTAGATTGCAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAA
ATTGCAGACTCACATGGAAGTGAGGAAAG
Found at i:29339 original size:34 final size:34
Alignment explanation
Indices: 29296--29363 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
29286 TAAATTGCAG
29296 ACTCACATGGAAGTGAGGAAATACCAACTTTGGC
1 ACTCACATGGAAGTGAGGAAATACCAACTTTGGC
29330 ACTCACATGGAAGTGAGGAAATACCAACTTTGGC
1 ACTCACATGGAAGTGAGGAAATACCAACTTTGGC
29364 CACTAAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (34 bp):
ACTCACATGGAAGTGAGGAAATACCAACTTTGGC
Found at i:29391 original size:81 final size:81
Alignment explanation
Indices: 29251--29410 Score: 257
Period size: 81 Copynumber: 2.0 Consensus size: 81
29241 GATTGTAGAA
* *
29251 TCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAAATTGCAGACTCACATGGAAGTGAGGAA
1 TCACATGGAAGCGAGAAAAGACCAACTTTGGCCACTAAATTGCAGACTCACATGGAAGTGAGGAA
*
29316 ATACCAACTTTGGCAC
66 AGACCAACTTTGGCAC
* * * *
29332 TCACATGGAAGTGAGGAAATACCAACTTTGGCCACTAAATTGCAGACTCACGTGGAAGTGAGGAA
1 TCACATGGAAGCGAGAAAAGACCAACTTTGGCCACTAAATTGCAGACTCACATGGAAGTGAGGAA
29397 AGACCAACTTTGGC
66 AGACCAACTTTGGC
29411 CACCAAATTG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (81 bp):
TCACATGGAAGCGAGAAAAGACCAACTTTGGCCACTAAATTGCAGACTCACATGGAAGTGAGGAA
AGACCAACTTTGGCAC
Found at i:29468 original size:175 final size:177
Alignment explanation
Indices: 29159--29508 Score: 517
Period size: 175 Copynumber: 2.0 Consensus size: 177
29149 TAAAGGCTCG
* *
29159 CATGGAAGCGAGAAAAAGACCAACTTTGGTCACTAAATTGTAGACTAGCGTGGAAGCGAGAAAAG
1 CATGGAAGCGAGAAAAAGACCAACTTTGGCCACTAAATTGCAGACTAGCGTGGAAGCGAGAAAAG
* * *
29224 ACCAACTTTGGTCACTAGATTGTAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAA
66 ACCAACTTTGGCCACCAAATTGTAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAA
* * *
29289 ATTGCAGACTCACATGGAAGTGAGGAAATACCAACTTTGG-CACTCA
131 ATTGCAGAATCACATGGAAGCGAGGAAAGACCAACTTTGGTCACTCA
* * * * *
29335 CATGGAAGTGAG-GAAATACCAACTTTGGCCACTAAATTGCAGACTCA-CGTGGAAGTGAGGAAA
1 CATGGAAGCGAGAAAAAGACCAACTTTGGCCACTAAATTGCAGACT-AGCGTGGAAGCGAGAAAA
* *
29398 GACCAACTTTGGCCACCAAATTGTAGAATCGCGTGGAAGCGAGGAAAGACCAACTTTGGTCACTA
65 GACCAACTTTGGCCACCAAATTGTAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTA
* *
29463 AATTGCAGAATCGCGTGGAAGCGAGGAAAGACCAACTTTGGTCACT
130 AATTGCAGAATCACATGGAAGCGAGGAAAGACCAACTTTGGTCACT
29509 AAATTGCAGA
Statistics
Matches: 155, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
175 139 0.90
176 16 0.10
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (177 bp):
CATGGAAGCGAGAAAAAGACCAACTTTGGCCACTAAATTGCAGACTAGCGTGGAAGCGAGAAAAG
ACCAACTTTGGCCACCAAATTGTAGAATCACGTGGAAGCGAGAAAAGACCAACTTTGGTCACTAA
ATTGCAGAATCACATGGAAGCGAGGAAAGACCAACTTTGGTCACTCA
Found at i:29903 original size:71 final size:70
Alignment explanation
Indices: 29697--29994 Score: 402
Period size: 71 Copynumber: 4.2 Consensus size: 70
29687 TTCATTTAAC
* * * *
29697 TTGGCTTATGGAAAAGCCCTCTG-ATGATTGGATGGAACCAATGATTAAACTGACTCGTATGGAA
1 TTGGCTTGTGGAAAAGCCC-CTGAATGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAA
29761 ACGAGT
65 ACGAGT
* * *
29767 TTGACTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTACGGAAA
1 TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAA
29832 CGAGT
66 CGAGT
* * * *
29837 TTGGCTTGTGGAAAAGCCCCCTGAATGCTTGGATGGAACTAAAGCTTGAACTGACTTGTATAGAA
1 TTGGCTTGTGGAAAAG-CCCCTGAATGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAA
*
29902 ACAAGT
65 ACGAGT
* *
29908 TTGGCTTGTGGAAAAGCCCCTGGAATGCTTGGATTGAACC-AAGACTTAAACTGACTTGTATGGA
1 TTGGCTTGTGGAAAAGCCCCT-GAATGCTTGGATGGAACCAAAG-CTTAAACTGACTCGTATGGA
29972 AACGAGT
64 AACGAGT
* *
29979 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
29995 TCAAAGCATT
Statistics
Matches: 204, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
69 3 0.01
70 82 0.40
71 119 0.58
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (70 bp):
TTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTAAACTGACTCGTATGGAAA
CGAGT
Found at i:29994 original size:142 final size:140
Alignment explanation
Indices: 29701--29994 Score: 410
Period size: 141 Copynumber: 2.1 Consensus size: 140
29691 TTTAACTTGG
* * * *
29701 CTTATGGAAAAGCCCTCTGATGATTGGATGGAACCAATGATTAAACTGACTCGTATGGAAACGAG
1 CTTATGGAAAAGCCCCCTGATGATTGGATGGAACCAAAGATTAAACTGACTCGTATAGAAACAAG
*
29766 TTTGACTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTACGGAA
66 TTTGACTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTAAACTGACTCGTACGGAA
*
29831 ACGAGTTTGG
131 ACGAGTTTGA
* * * * * *
29841 CTTGTGGAAAAGCCCCCTGAATGCTTGGATGGAACTAAAGCTTGAACTGACTTGTATAGAAACAA
1 CTTATGGAAAAGCCCCCTG-ATGATTGGATGGAACCAAAGATTAAACTGACTCGTATAGAAACAA
* * * *
29906 GTTTGGCTTGTGGAAAAGCCCCTGGAATGCTTGGATTGAACC-AAGACTTAAACTGACTTGTATG
65 GTTTGACTTGTGGAAAAGCCCCT-GAATGCTTGGATGGAACCAAAG-CTTAAACTGACTCGTACG
29970 GAAACGAGTTTGA
128 GAAACGAGTTTGA
29983 CTTATGGAAAAG
1 CTTATGGAAAAG
29995 TCAAAGCATT
Statistics
Matches: 134, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
140 17 0.13
141 62 0.46
142 55 0.41
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (140 bp):
CTTATGGAAAAGCCCCCTGATGATTGGATGGAACCAAAGATTAAACTGACTCGTATAGAAACAAG
TTTGACTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTAAACTGACTCGTACGGAA
ACGAGTTTGA
Found at i:30657 original size:50 final size:50
Alignment explanation
Indices: 30527--30673 Score: 213
Period size: 50 Copynumber: 2.9 Consensus size: 50
30517 ATGCCCTTTG
* * ** * * *
30527 AAAAGCAAATTTTGGTATTGGACTCACAAACAGAAAGCAAACTTATTTTG
1 AAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTC
* *
30577 AAAAGCGAATTTTGATCATGGACTCACAAATGGAATGCAATCTTATTTTC
1 AAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTC
30627 AAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATT
1 AAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATT
30674 ATAAAACTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 86 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (50 bp):
AAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATTTTC
Found at i:31706 original size:1 final size:1
Alignment explanation
Indices: 31702--31758 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
31692 TTTTTCTTCC
* * * * ** *
31702 TTTTTTTTTTCTTTTTTTCTTTTCTTTTTTTTTCTTTTTTCCTTTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
31759 CATTCATTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:31710 original size:15 final size:13
Alignment explanation
Indices: 31690--31758 Score: 66
Period size: 13 Copynumber: 4.9 Consensus size: 13
31680 TTCCAAGTGC
31690 TTTTTTTCTTCCTTT
1 TTTTTTTCTT--TTT
31705 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
*
31718 TTCTTTTCTTTTT
1 TTTTTTTCTTTTT
*
31731 TTTTCTTTTTTCCTTT
1 TTTT-TTTCTT--TTT
*
31747 TTTTTTTATTTT
1 TTTTTTTCTTTT
31759 CATTCATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
13 20 0.43
14 5 0.11
15 15 0.32
16 7 0.15
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:31719 original size:23 final size:23
Alignment explanation
Indices: 31689--31758 Score: 85
Period size: 21 Copynumber: 3.2 Consensus size: 23
31679 ATTCCAAGTG
31689 CTTTTTTTCTTCCTTTTTTTTTT
1 CTTTTTTTCTTCCTTTTTTTTTT
*
31712 CTTTTTTTCTT--TTCTTTTTTT
1 CTTTTTTTCTTCCTTTTTTTTTT
*
31733 -TTCTTTT-TTCCTTTTTTTTTT
1 CTTTTTTTCTTCCTTTTTTTTTT
*
31754 ATTTT
1 CTTTT
31759 CATTCATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.05
20 6 0.15
21 18 0.45
22 3 0.08
23 11 0.28
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (23 bp):
CTTTTTTTCTTCCTTTTTTTTTT
Found at i:31728 original size:24 final size:24
Alignment explanation
Indices: 31689--31759 Score: 94
Period size: 23 Copynumber: 3.0 Consensus size: 24
31679 ATTCCAAGTG
*
31689 CTTTTTTTC-TTCCTTTTTTTTTT
1 CTTTTTTTCTTTTCTTTTTTTTTT
31712 CTTTTTTTCTTTTC-TTTTTTTTT
1 CTTTTTTTCTTTTCTTTTTTTTTT
*
31735 CTTTTTTCCTTTT-TTTTTTATTTT
1 CTTTTTTTCTTTTCTTTTTT-TTTT
31759 C
1 C
31760 ATTCATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 35 0.81
24 8 0.19
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (24 bp):
CTTTTTTTCTTTTCTTTTTTTTTT
Found at i:31730 original size:34 final size:34
Alignment explanation
Indices: 31692--31759 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
31682 CCAAGTGCTT
* *
31692 TTTTTCTTCCTTTTTT-TTTTCTTTTTTTCTTTTC
1 TTTTTCTTCCTTTTTTCCTTT-TTTTTTTATTTTC
* *
31726 TTTTTTTTTCTTTTTTCCTTTTTTTTTTATTTTC
1 TTTTTCTTCCTTTTTTCCTTTTTTTTTTATTTTC
31760 ATTCATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (34 bp):
TTTTTCTTCCTTTTTTCCTTTTTTTTTTATTTTC
Found at i:31751 original size:12 final size:11
Alignment explanation
Indices: 31689--31759 Score: 65
Period size: 12 Copynumber: 6.1 Consensus size: 11
31679 ATTCCAAGTG
*
31689 CTTTTTTTCTTC
1 CTTTTTTT-TTT
31701 CTTTTTTTTTT
1 CTTTTTTTTTT
31712 CTTTTTTTCTTT
1 CTTTTTTT-TTT
31724 -TCTTTTTTTTT
1 CT-TTTTTTTTT
31735 CTTTTTTCCTTTT
1 CTTTTTT--TTTT
31748 -TTTTTTATTTT
1 CTTTTTT-TTTT
31759 C
1 C
31760 ATTCATTTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
11 23 0.45
12 24 0.47
13 4 0.08
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:37089 original size:292 final size:293
Alignment explanation
Indices: 36561--37149 Score: 1090
Period size: 292 Copynumber: 2.0 Consensus size: 293
36551 TAATTTGTCC
36561 AAGTTAGTAATTAAATTTACTAATTAGGTGAAAATCAAGAATACATGTAATAAAGCATTTTTGCA
1 AAGTTAGTAATTAAATTTACTAATTAGGTGAAAATCAAGAATACATGTAATAAAGCATTTTTGCA
*
36626 TCCATGTTCATGCATTTAAATTTCTTTAAATGTTGTTGATGCCATGCTCATTTGAGAAAAACAAA
66 TCCATGTTCATGCATTTAAATTTCTTTAAATGTTGTTGATGCCATGCTC---TGAGAAAAAAAAA
* *
36691 TCGACACCGATGATGGAATAATAGGTTGAAATTTAGACAACATTTGTCCATTTCAATCTGAGTTT
128 TCGACACCGATGATGGAATAATAGGTTGAAATGTAGACAACATTTGTCCATTTAAATCTGAGTTT
36756 CCTAGGCTTGAGACATCTAAATGGGAGTCTTACCAATCAAGTGGAAGGTGCCCAAATAGTGTCTC
193 CCTAGGCTTGAGACATCTAAATGGGAGTCTTACCAATCAAGTGGAAGGTGCCCAAATAGTGTCTC
*
36821 TCGTATAACTACATGGTAAAATATGTTTAAACCGGA
258 TCGTATAACTACATAGTAAAATATGTTTAAACCGGA
36857 AAGTTAGTAATTAAATTTACTAATTAGGTGAAAATCAAGAATACATGTAATAAAGCATTTTTGCA
1 AAGTTAGTAATTAAATTTACTAATTAGGTGAAAATCAAGAATACATGTAATAAAGCATTTTTGCA
*
36922 TCCATGTTCATGCATTTAAATTTCTTTAAATGTTGTTGATGTCATGCTC-GAGAAAAAAAAATCG
66 TCCATGTTCATGCATTTAAATTTCTTTAAATGTTGTTGATGCCATGCTCTGAGAAAAAAAAATCG
*
36986 ACACCGATGATGGAATAATCGGTTGAAATGTAGACAACATTTGTCCATTTAAATCTGAGTTTCCT
131 ACACCGATGATGGAATAATAGGTTGAAATGTAGACAACATTTGTCCATTTAAATCTGAGTTTCCT
37051 AGGCTTGAGACATCTAAATGGGAGTCTTACCAATCAAGTGGAAGGTGCCCAAATAGTGTCTCTCG
196 AGGCTTGAGACATCTAAATGGGAGTCTTACCAATCAAGTGGAAGGTGCCCAAATAGTGTCTCTCG
37116 TATAACTACATAGTAAAATATGTTTAAACCGGA
261 TATAACTACATAGTAAAATATGTTTAAACCGGA
37149 A
1 A
37150 TACATGCATC
Statistics
Matches: 287, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
292 174 0.61
296 113 0.39
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (293 bp):
AAGTTAGTAATTAAATTTACTAATTAGGTGAAAATCAAGAATACATGTAATAAAGCATTTTTGCA
TCCATGTTCATGCATTTAAATTTCTTTAAATGTTGTTGATGCCATGCTCTGAGAAAAAAAAATCG
ACACCGATGATGGAATAATAGGTTGAAATGTAGACAACATTTGTCCATTTAAATCTGAGTTTCCT
AGGCTTGAGACATCTAAATGGGAGTCTTACCAATCAAGTGGAAGGTGCCCAAATAGTGTCTCTCG
TATAACTACATAGTAAAATATGTTTAAACCGGA
Found at i:37234 original size:27 final size:28
Alignment explanation
Indices: 37196--37253 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 28
37186 GAACACAGTT
37196 AAGGACTTAATTCAGGCAAATTAAG-AA
1 AAGGACTTAATTCAGGCAAATTAAGTAA
*
37223 AAGGACTTAATTCAGGGAAATTAAGTAA
1 AAGGACTTAATTCAGGCAAATTAAGTAA
37251 AAG
1 AAG
37254 CAGTAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22
Consensus pattern (28 bp):
AAGGACTTAATTCAGGCAAATTAAGTAA
Found at i:37269 original size:36 final size:36
Alignment explanation
Indices: 37226--38397 Score: 597
Period size: 36 Copynumber: 31.7 Consensus size: 36
37216 TTAAGAAAAG
*
37226 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAA
1 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
* *
37262 GACTTAATTCAGGGAAATTAGGTAAAAGCAGTAAAA
1 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
* * *
37298 GGACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAA
1 -GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
* * *
37335 GGACTTAATTCAGGGTAATTAAGTAAAAGCGGTCAAG
1 -GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
* *
37372 GACTTAATTAAGGGAAATTAAGTAAAAGCAAT-AAA
1 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
* *
37407 GGACTTAATTCAGGGTAATTAAGTAAACA-TAGT-AAA
1 -GACTTAATTCAGGGAAATTAAGTAAA-AGCAGTCAAA
* * *
37443 GAACTTAATTTAGGGTAATTAAGTAAAAGCAGTTAAA
1 G-ACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
* * *
37480 GGACTTAATTCAGGGTAATTAAGTAAAAAACAGTCAAG
1 -GACTTAATTCAGGGAAATTAAGT-AAAAGCAGTCAAA
* * * *
37518 GACTTAATTCAAGGTAATTAGGT-AAAGACAAG-CACA
1 GACTTAATTCAGGGAAATTAAGTAAAAG-C-AGTCAAA
* * *
37554 GACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAG-CACA
1 GACTTAA-TTC-A-G--GGAAATTAAGTAAAAGC-AGTCAAA
* * *
37595 TACTTAATTTCAAGGAAGGAAATTAGGT-AAA-CAAGT-ACA
1 GACTTAA-TTC-A-G--GGAAATTAAGTAAAAGC-AGTCAAA
* *
37634 GACTTAATTTCTAGGAAGGAAATTAGGT-AAAGACAAG-CACA
1 GACTTAA-TTC-A-G--GGAAATTAAGTAAAAG-C-AGTCAAA
* *
37675 GACTTAATTTCAAGGAAGGAAATTAGGT-AAAGACAAG-CACA
1 GACTTAA-TTC-A-G--GGAAATTAAGTAAAAG-C-AGTCAAA
* * *
37716 GACTTAATTTCAAGGAAGGAAATTAAGTACAGGCAAGT-ATA
1 GACTTAA-TTC-A-G--GGAAATTAAGTAAAAGC-AGTCAAA
**
37757 GACTTAATTCA-GGATAATTAAGT-AATTCAG-CAAA
1 GACTTAATTCAGGGA-AATTAAGTAAAAGCAGTCAAA
** * *
37791 GACTTAATTTCA-CAAGAATTAAGTAAAATCA-ACAAA
1 GACTTAA-TTCAGGGA-AATTAAGTAAAAGCAGTCAAA
** *
37827 GACTTAATTTCA-CAAGAATTAAGTAAAATCAG-CAAA
1 GACTTAA-TTCAGGGA-AATTAAGTAAAAGCAGTCAAA
** * * *
37863 GACTTAA-TCTAAAGATGATTAAGTAAGATCAGTCAAA
1 GACTTAATTC-AGGGA-AATTAAGTAAAAGCAGTCAAA
* ** *
37900 AACTTAACCCAAGGG-GATTAAGT---AG-AGTCAAA
1 GACTTAATTC-AGGGAAATTAAGTAAAAGCAGTCAAA
* *
37932 GACTTAATTTCAAGGAAGGAAATTAAGT---AG-AATCAAT
1 GACTTAA-TTC-A-G--GGAAATTAAGTAAAAGCAGTCAAA
* *** * * * *
37969 GACTTAATTTCAAGGAAGGAAATTAAATGAAGTCAAG
1 GACTTAA-TTCAGGGAAATTAAGTAAAAGCAGTCAAA
*
38006 GACTTAATTTCAAGGAAGGAAATTAAGT--AA--AGTCAAG
1 GACTTAA-TTC-A-G--GGAAATTAAGTAAAAGCAGTCAAA
** * * **
38043 GACTTAATTTCAGGG-AAGGAAAT-TAAGTCAAGTCAGG
1 GACTTAA-TTCAGGGAAATTAAGTAAAAG-C-AGTCAAA
* *
38080 GACTTAATTCAGGGTAATTAAGTAAAAGCAGTAAAA
1 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
*
38116 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAA
1 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
* * *
38152 GGACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAA
1 -GACTTAATTCAGGGAAATTAAGTAAAAGCAG-TCAAA
* * *
38190 GACTTAATTCAGGGTAATTAAGTAAAAGCGGTCAAG
1 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
*
38226 GACTTACTTCAGGGAAATTAAGTAAAAGCAGT-AAA
1 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
* * *
38261 TGACTTAATTCAGGGTAATTAAGTAAACA-TAGT-AAG
1 -GACTTAATTCAGGGAAATTAAGTAAA-AGCAGTCAAA
* *
38297 GAACTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAA
1 G-ACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
** * *
38334 GGACTTAATTCAGGTTAATTAAGTAAAAAACAGTCAAG
1 -GACTTAATTCAGGGAAATTAAGT-AAAAGCAGTCAAA
* * *
38372 GACTTAATTCAAGGTAATTAGGTAAA
1 GACTTAATTCAGGGAAATTAAGTAAA
38398 GACAAACAGA
Statistics
Matches: 961, Mismatches: 114, Indels: 122
0.80 0.10 0.10
Matches are distributed among these distances:
32 18 0.02
33 15 0.02
34 14 0.01
35 31 0.03
36 354 0.37
37 306 0.32
38 35 0.04
39 38 0.04
40 6 0.01
41 139 0.14
42 5 0.01
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.25
Consensus pattern (36 bp):
GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAA
Found at i:37560 original size:182 final size:182
Alignment explanation
Indices: 37222--38397 Score: 554
Period size: 182 Copynumber: 6.4 Consensus size: 182
37212 CAAATTAAGA
*
37222 AAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAAGACTTAATTCAGGGAAATTAGGTAA
1 AAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAAGACTTAATTCAGGGAAATTAAGTAA
*
37287 AAGCAGTAAAAGGACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAGGACTTAATTCAGGGTA
66 AAGCAGTAAAAGGACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAGGACTTAATTCAAGGTA
*
37352 ATTAAGTAAAAGCGGTCAAGGACTTAATTAAGGGAAATTAAGTAAAAGCAAT
131 ATTAAGTAAAAGCAGTCAAGGACTTAATTAAGGGAAATTAAGTAAAAGCAAT
* * * *
37404 AAAGGACTTAATTCAGGGTAATTAAGTAAACA-TAGT-AAAGAACTTAATTTAGGGTAATTAAGT
1 AAAGGACTTAATTCAGGGAAATTAAGTAAA-AGCAGTAAAAG-ACTTAATTCAGGGAAATTAAGT
* *
37467 AAAAGCAGTTAAAGGACTTAATTCAGGGTAATTAAGTAAAAAACAG-TCAAGGACTTAATTCAAG
64 AAAAGCAGTAAAAGGACTTAATTCAGGGTAATTAAGT-AAAAACAGTTAAAGGACTTAATTCAAG
* * * *
37531 GTAATTAGGT-AAAGACAAG-CACA-GACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGC
128 GTAATTAAGTAAAAG-C-AGTCA-AGGACTTAA-TT-AA-G--GGAAATTAAGTAAAAGCAA-T
* * * *
37592 ACA-TACTTAATTTCAAGGAAGGAAATTAGGT-AAA-CAAGT-ACAGACTTAATTTCTAGGAAGG
1 AAAGGACTTAA-TTC-A-G--GGAAATTAAGTAAAAGC-AGTAAAAGACTTAA-TTC-A-G--GG
* * * * * * *
37653 AAATTAGGT-AAAGACAAG-CACA-GACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAG-CA
55 AAATTAAGTAAAAG-C-AGTAAAAGGACTTAA-TTC-A-G--GGTAATTAAGTAAAAAC-AGTTA
* * * * *
37714 CA-GACTTAATTTCAAGGAAGGAAATTAAGTACAGGCAAGT-ATA-GACTTAATTCA-GGATAAT
112 AAGGACTTAA-TTC----AAGGTAATTAAGTAAAAGC-AGTCA-AGGACTTAATTAAGGGA-AAT
** **
37775 TAAGT-AATTCAGC
169 TAAGTAAAAGCAAT
** * **
37788 AAA-GACTTAATTTCA-CAAGAATTAAGTAAAATCA--ACAAAGACTTAATTTCA-CAAGAATTA
1 AAAGGACTTAA-TTCAGGGA-AATTAAGTAAAAGCAGTA-AAAGACTTAA-TTCAGGGA-AATTA
* * * * * * * * * * **
37848 AGTAAAATCAG-CAAA-GACTTAATCTAAAGATGATTAAGTAAGATCAGTCAAA-AACTTAACCC
61 AGTAAAAGCAGTAAAAGGACTTAAT-TCAGGGTAATTAAGTAAAAACAGTTAAAGGACTTAATTC
** *
37910 AAGGGGATTAAGT---AG-AGTCAAAGACTTAATTTCAAGGAAGGAAATTAAGT---AG-AAT
125 AAGGTAATTAAGTAAAAGCAGTCAAGGACTTAA-TT-AA-G--GGAAATTAAGTAAAAGCAAT
* * * *** * * * * *
37965 CAATGACTTAATTTCAAGGAAGGAAATTAAATGAAGTCAAGGACTTAATTTCAAGGAAGGAAATT
1 AAAGGACTTAA-TTCAGGGAAATTAAGTAAAAGCAGTAAAAGACTTAA-TTC-A-G--GGAAATT
* ** * * ** * *
38030 AAGT--AA--AGT-CAAGGACTTAATTTCAGGG-AAGGAAATTAAGTCAAG-TCAGGGACTTAAT
60 AAGTAAAAGCAGTAAAAGGACTTAA-TTCAGGGTAATTAAGTAAAAAC-AGTTAAAGGACTTAAT
* * * * *
38088 TCAGGGTAATTAAGTAAAAGCAGTAAAAGACTTAATTCAGGGAAATTAAGTAAAAGCAGT
123 TCAAGGTAATTAAGTAAAAGCAGTCAAGGACTTAATTAAGGGAAATTAAGTAAAAGCAAT
* * *
38148 AAAAGGACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAAGACTTAATTCAGGGTAATTAAGT
1 -AAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAG-TAAAAGACTTAATTCAGGGAAATTAAGT
* * * * * * *
38213 AAAAGCGGT-CAAGGACTTACTTCAGGGAAATTAAGTAAAAGCAG-TAAATGACTTAATTCAGGG
64 AAAAGCAGTAAAAGGACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAGGACTTAATTCAAGG
* * * *
38276 TAATTAAGTAAACA-TAGT-AAGGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
129 TAATTAAGTAAA-AGCAGTCAAGG-ACTTAATTAAGGGAAATTAAGTAAAAGCA-AT
** * * * * * *
38331 AAAGGACTTAATTCAGGTTAATTAAGTAAAAAACAGTCAAGGACTTAATTCAAGGTAATTAGGTA
1 AAAGGACTTAATTCAGGGAAATTAAGT-AAAAGCAGTAAAAGACTTAATTCAGGGAAATTAAGTA
38396 AA
65 AA
38398 GACAAACAGA
Statistics
Matches: 762, Mismatches: 143, Indels: 178
0.70 0.13 0.16
Matches are distributed among these distances:
174 4 0.01
175 8 0.01
176 3 0.00
177 4 0.01
178 20 0.03
179 58 0.08
180 38 0.05
181 21 0.03
182 247 0.32
183 78 0.10
184 54 0.07
185 1 0.00
187 25 0.03
188 19 0.02
189 9 0.01
190 11 0.01
191 11 0.01
192 18 0.02
193 18 0.02
194 12 0.02
195 16 0.02
196 16 0.02
197 8 0.01
198 19 0.02
199 15 0.02
201 1 0.00
202 2 0.00
203 24 0.03
204 2 0.00
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.25
Consensus pattern (182 bp):
AAAGGACTTAATTCAGGGAAATTAAGTAAAAGCAGTAAAAGACTTAATTCAGGGAAATTAAGTAA
AAGCAGTAAAAGGACTTAATTCAGGGTAATTAAGTAAAAACAGTTAAAGGACTTAATTCAAGGTA
ATTAAGTAAAAGCAGTCAAGGACTTAATTAAGGGAAATTAAGTAAAAGCAAT
Found at i:37580 original size:41 final size:41
Alignment explanation
Indices: 37528--37765 Score: 372
Period size: 41 Copynumber: 5.9 Consensus size: 41
37518 GACTTAATTC
*
37528 AAGGTAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* *
37569 AAGGAAATTAGGTAAAAACAAGCACATACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* *
37610 AAGGAAATTAGGT-AA-ACAAGTACAGACTTAATTTCTAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
37649 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
37690 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* * * * *
37731 AAGGAAATTAAGTACAGGCAAGTATAGACTTAATT
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
37766 CAGGATAATT
Statistics
Matches: 182, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 34 0.19
40 4 0.02
41 144 0.79
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (41 bp):
AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
Found at i:37644 original size:80 final size:82
Alignment explanation
Indices: 37528--37740 Score: 367
Period size: 80 Copynumber: 2.6 Consensus size: 82
37518 GACTTAATTC
*
37528 AAGGTAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
*
37593 CATACTTAATTTCAAGG
66 CAGACTTAATTTCAAGG
* * *
37610 AAGGAAATTAGGT-AA-ACAAGTACAGACTTAATTTCTAGGAAGGAAATTAGGTAAAGACAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
37673 CAGACTTAATTTCAAGG
66 CAGACTTAATTTCAAGG
37690 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTA
37741 AGTACAGGCA
Statistics
Matches: 122, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
80 74 0.61
81 4 0.03
82 44 0.36
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (82 bp):
AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
CAGACTTAATTTCAAGG
Found at i:37668 original size:121 final size:123
Alignment explanation
Indices: 37528--38699 Score: 451
Period size: 121 Copynumber: 10.3 Consensus size: 123
37518 GACTTAATTC
*
37528 AAGGTAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
* *
37593 CATACTTAATTTCAAGGAAGGAAATTAGGTA-A-ACAAGTACAGACTTAATTTCTAGG
66 CAGACTTAATTTCAAGGAAGGAAATTAAGTACAGACAAGTACAGACTTAATTTCTAGG
*
37649 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
* *
37714 CAGACTTAATTTCAAGGAAGGAAATTAAGTACAGGCAAGTATAGACTTAA-TTC-AGG
66 CAGACTTAATTTCAAGGAAGGAAATTAAGTACAGACAAGTACAGACTTAATTTCTAGG
* * ** * * * *
37770 -A--TAATTAAGT-AATTC-AGCAAAGACTTAATTTC-A-CAA-G-AATTAAGTAAAATCAA-CA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
* * * * *
37825 AAGACTTAATTTC-A-CAA-G-AATTAAGTA-AAATC-AGCAAAGACTTAA--TCTA--
66 CAGACTTAATTTCAAGGAAGGAAATTAAGTACAGA-CAAGTACAGACTTAATTTCTAGG
* * * * ** * * **
37874 AA-GATGATTAAGT-AAGATC-AGTCAAAAACTTAA-CCCAAGG--GG--ATTAAGTAGAGTC-A
1 AAGGA-AATTAGGTAAAGA-CAAG-CACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAA
* *
37930 --A-AGACTTAATTTCAAGGAAGGAAATTAAGTAGA-ATCAA-T---GACTTAATTTCAAGG
63 GCACAGACTTAATTTCAAGGAAGGAAATTAAGTACAGA-CAAGTACAGACTTAATTTCTAGG
** * * * **
37984 AAGGAAATTAAATGAAGTCAAG----GACTTAATTTCAAGGAAGGAAATTAAGTAAAGTCAAG--
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
*
38043 --GACTTAATTTCAGGGAAGGAAATTAAGT-----CAAGT-CAGGGACTTAA-TTC-A-G
66 CAGACTTAATTTCAAGGAAGGAAATTAAGTACAGACAAGTACA--GACTTAATTTCTAGG
* * * * * *
38092 --GGTAATTAAGTAAA-AGC-AGTAAAAGACTTAA-TTC-A-G--GGAAATTAAGTAAAAGC-AG
1 AAGGAAATTAGGTAAAGA-CAAG-CACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAG
* * * * * *
38147 TAAAAGGACTTAA-TTC-A-G--GGTAATTAAGTAAAAAC-AGTTAAAAGACTTAA-TTC-A-G
64 -CACA-GACTTAATTTCAAGGAAGGAAATTAAGTACAGACAAG-T-ACAGACTTAATTTCTAGG
* * * * * *
38202 --GGTAATTAAGTAAA-AGC-GGTCA-AGGACTT-ACTTC-A-G--GGAAATTAAGTAAAAGC-A
1 AAGGAAATTAGGTAAAGA-CAAG-CACA-GACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAA
* * *
38256 GTAAATGACTTAA-TTC-A-G--GGTAATTAAGTA-A-ACATAGTA-AGGAACTTAA-TTC-A-G
63 GCACA-GACTTAATTTCAAGGAAGGAAATTAAGTACAGACA-AGTACA-G-ACTTAATTTCTAGG
* * * * ** *
38310 --GGTAATTAAGTAAA-AGC-AGTTAAAGGACTTAA-TTC-A-G--GTTAATTAAGTAAAAA-AC
1 AAGGAAATTAGGTAAAGA-CAAG-CACA-GACTTAATTTCAAGGAAGGAAATTAGGTAAAAACA-
* * * ** * *
38365 AGTCA-AGGACTTAA-TTC----AAGGTAATTAGGTAAAGACAAACAGAGACTTAATTTCAAGG
62 AG-CACA-GACTTAATTTCAAGGAAGGAAATTAAGTACAGACAAGTACAGACTTAATTTCTAGG
*
38423 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATCAGGT--AAACAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
* * * *
38486 CAGACTTAATTTTTAA-GAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCTAGG
66 CAGACTTAA-TTTCAAGGAAGGAAATTAAGTACAGACAAGTACAGACTTAATTTCTAGG
* * *
38544 AAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTAAAGGAAGGAAATTAGGT--AAACAAGAA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
* * * * *
38607 CAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
66 CAGACTTAATTTCAAGGAAGGAAATTAAGTACAGACAAGTACAGACTTAATTTCTAGG
* * *
38665 AAGGAAATTAAGTAAAGGCAAGCATAGACTTAATT
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
38700 CAGGGTAATT
Statistics
Matches: 869, Mismatches: 89, Indels: 186
0.76 0.08 0.16
Matches are distributed among these distances:
104 2 0.00
105 42 0.05
106 44 0.05
107 34 0.04
108 55 0.06
109 93 0.11
110 123 0.14
111 75 0.09
112 20 0.02
113 2 0.00
114 9 0.01
115 19 0.02
116 29 0.03
117 10 0.01
118 10 0.01
119 7 0.01
120 6 0.01
121 271 0.31
122 4 0.00
123 14 0.02
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.24
Consensus pattern (123 bp):
AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAACAAGCA
CAGACTTAATTTCAAGGAAGGAAATTAAGTACAGACAAGTACAGACTTAATTTCTAGG
Found at i:37828 original size:21 final size:21
Alignment explanation
Indices: 37804--37869 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
37794 TTAATTTCAC
37804 AAGAATTAAGTAAAATCAACA
1 AAGAATTAAGTAAAATCAACA
* *
37825 AAGACTTAA-T---TTC-AC-
1 AAGAATTAAGTAAAATCAACA
*
37840 AAGAATTAAGTAAAATCAGCA
1 AAGAATTAAGTAAAATCAACA
*
37861 AAGACTTAA
1 AAGAATTAA
37870 TCTAAAGATG
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
15 8 0.24
16 3 0.09
17 2 0.06
19 2 0.06
20 2 0.06
21 16 0.48
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.23
Consensus pattern (21 bp):
AAGAATTAAGTAAAATCAACA
Found at i:38026 original size:74 final size:74
Alignment explanation
Indices: 37925--38088 Score: 258
Period size: 74 Copynumber: 2.2 Consensus size: 74
37915 GATTAAGTAG
* *
37925 AGTCAAAGACTTAATTTCAAGGAAGGAAATTAAGTAGAA-TCAATGACTTAATTTCAAGGAAGGA
1 AGTCAAGGACTTAATTTCAAGGAAGGAAATTAAGTA-AAGTCAAGGACTTAATTTCAAGGAAGGA
*
37989 AATTAAATGA
65 AATTAAATCA
*
37999 AGTCAAGGACTTAATTTCAAGGAAGGAAATTAAGTAAAGTCAAGGACTTAATTTCAGGGAAGGAA
1 AGTCAAGGACTTAATTTCAAGGAAGGAAATTAAGTAAAGTCAAGGACTTAATTTCAAGGAAGGAA
*
38064 ATTAAGTCA
66 ATTAAATCA
*
38073 AGTCAGGGACTTAATT
1 AGTCAAGGACTTAATT
38089 CAGGGTAATT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
73 2 0.02
74 81 0.98
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (74 bp):
AGTCAAGGACTTAATTTCAAGGAAGGAAATTAAGTAAAGTCAAGGACTTAATTTCAAGGAAGGAA
ATTAAATCA
Found at i:38434 original size:41 final size:41
Alignment explanation
Indices: 38382--38699 Score: 475
Period size: 41 Copynumber: 7.9 Consensus size: 41
38372 GACTTAATTC
* * *
38382 AAGGTAATTAGGTAAAGACAAACAGAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
38423 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* *
38464 AAGGAAATCAGGT-AA-ACAAGCACAGACTTAATTTTTAA-G
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAA-TTTCAAGG
*
38503 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCTAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* *
38544 AAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTAAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* *
38585 AAGGAAATTAGGT-AA-ACAAGAACAAACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
38624 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
* * *
38665 AAGGAAATTAAGTAAAGGCAAGCATAGACTTAATT
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
38700 CAGGGTAATT
Statistics
Matches: 251, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
39 62 0.25
40 17 0.07
41 172 0.69
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (41 bp):
AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGG
Found at i:38507 original size:80 final size:82
Alignment explanation
Indices: 38382--38699 Score: 475
Period size: 80 Copynumber: 3.9 Consensus size: 82
38372 GACTTAATTC
* * *
38382 AAGGTAATTAGGTAAAGACAAACAGAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCA
38447 CAGACTTAATTTCAAGG
66 CAGACTTAATTTCAAGG
* *
38464 AAGGAAATCAGGT-AA-ACAAGCACAGACTTAATTTTTAA-GAAGGAAATTAGGTAAAGACAAGC
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAA-TTTCAAGGAAGGAAATTAGGTAAAGACAAGC
*
38526 ACAGACTTAATTTCTAGG
65 ACAGACTTAATTTCAAGG
* * *
38544 AAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTAAAGGAAGGAAATTAGGT-AA-ACAAGAA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCA
*
38607 CAAACTTAATTTCAAGG
66 CAGACTTAATTTCAAGG
* *
38624 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAAGTAAAGGCAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCA
*
38689 TAGACTTAATT
66 CAGACTTAATT
38700 CAGGGTAATT
Statistics
Matches: 211, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
80 139 0.66
81 18 0.09
82 54 0.26
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (82 bp):
AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCA
CAGACTTAATTTCAAGG
Found at i:38764 original size:36 final size:36
Alignment explanation
Indices: 38706--38804 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
38696 AATTCAGGGT
38706 AATTAAGT-AAATCAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTTCACAAG
*
38741 AATTAAGTAAAACCAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTTCACAAG
*
38777 AATTAAGTAAAATCAGCAAAGAATTAAT
1 AATTAAGTAAAATCAGCAAAGACTTAAT
38805 CGAAAGATGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 8 0.13
36 52 0.87
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (36 bp):
AATTAAGTAAAATCAGCAAAGACTTAATTTCACAAG
Found at i:38800 original size:21 final size:21
Alignment explanation
Indices: 38738--38803 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
38728 TTAATTTCAC
*
38738 AAGAATTAAGTAAAACCAGCA
1 AAGAATTAAGTAAAATCAGCA
* *
38759 AAGACTTAA-T---TTCA-C-
1 AAGAATTAAGTAAAATCAGCA
38774 AAGAATTAAGTAAAATCAGCA
1 AAGAATTAAGTAAAATCAGCA
38795 AAGAATTAA
1 AAGAATTAA
38804 TCGAAAGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
15 8 0.24
16 2 0.06
17 2 0.06
19 3 0.09
20 2 0.06
21 17 0.50
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (21 bp):
AAGAATTAAGTAAAATCAGCA
Found at i:38818 original size:36 final size:35
Alignment explanation
Indices: 38670--38840 Score: 161
Period size: 36 Copynumber: 4.8 Consensus size: 35
38660 CAAGGAAGGA
** * **
38670 AATTAAGTAAAGGCAAGCATAGACTTAATTCA-GGG
1 AATTAAGTAAAATC-AGCAAAGACTTAATTCACAAG
38705 TAATTAAGT-AAATCAGCAAAGACTTAATTTCACAAG
1 -AATTAAGTAAAATCAGCAAAGACTTAA-TTCACAAG
*
38741 AATTAAGTAAAACCAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATCAGCAAAGACTTAA-TTCACAAG
*
38777 AATTAAGTAAAATCAGCAAAGAATTAA-TCGA-AAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTC-ACAAG
* *
38811 ATGATTAAGTAAGATCAGTCAAAAACTTAA
1 A--ATTAAGTAAAATCAG-CAAAGACTTAA
38841 CCCAAGGGGA
Statistics
Matches: 117, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
34 18 0.15
35 16 0.14
36 74 0.63
37 9 0.08
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (35 bp):
AATTAAGTAAAATCAGCAAAGACTTAATTCACAAG
Found at i:38893 original size:37 final size:37
Alignment explanation
Indices: 38850--39022 Score: 276
Period size: 37 Copynumber: 4.7 Consensus size: 37
38840 ACCCAAGGGG
*
38850 ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAAGAAA
1 ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAAGGAA
* *
38887 ATTAAGTAGAATCAATGACTTAATTTCAAGGAAGGAA
1 ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAAGGAA
*
38924 ATTAAGTAGAGTCAAGGACTTAATTTTAAGGAAGGAA
1 ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAAGGAA
*
38961 ATTAAGTAGAGTCAAGGACTTAATTTTAAGGAAGGAA
1 ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAAGGAA
*
38998 ATTAAGTCA-AGTCAGGGACTTAATT
1 ATTAAGT-AGAGTCAAGGACTTAATT
39023 CAGGGTAATT
Statistics
Matches: 128, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
37 127 0.99
38 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (37 bp):
ATTAAGTAGAGTCAAGGACTTAATTTCAAGGAAGGAA
Found at i:38940 original size:19 final size:19
Alignment explanation
Indices: 38918--38978 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
38908 AATTTCAAGG
38918 AAGGAAATTAAGTAGAGTC
1 AAGGAAATTAAGTAGAGTC
* * *
38937 AAGG-ACTTAATTTTA-AG-G
1 AAGGAAATTAA--GTAGAGTC
38955 AAGGAAATTAAGTAGAGTC
1 AAGGAAATTAAGTAGAGTC
38974 AAGGA
1 AAGGA
38979 CTTAATTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
17 2 0.06
18 11 0.35
19 16 0.52
20 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (19 bp):
AAGGAAATTAAGTAGAGTC
Found at i:38958 original size:18 final size:18
Alignment explanation
Indices: 38937--38996 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
38927 AAGTAGAGTC
38937 AAGGACTTAATTTTAAGG
1 AAGGACTTAATTTTAAGG
* * *
38955 AAGGAAATTAA--GTAGAGTC
1 AAGG-ACTTAATTTTA-AG-G
38974 AAGGACTTAATTTTAAGG
1 AAGGACTTAATTTTAAGG
38992 AAGGA
1 AAGGA
38997 AATTAAGTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
17 2 0.06
18 16 0.52
19 11 0.35
20 2 0.06
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (18 bp):
AAGGACTTAATTTTAAGG
Found at i:39059 original size:36 final size:37
Alignment explanation
Indices: 39015--39201 Score: 258
Period size: 36 Copynumber: 5.2 Consensus size: 37
39005 CAAGTCAGGG
* *
39015 ACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAG-
1 ACTTAATTCAGGGTAATTAAGTCGAGTCAATAAAAGA
* * * *
39051 GCTTAATTCAGGGTAATTAAGTGGATTCAAT-AAAGG
1 ACTTAATTCAGGGTAATTAAGTCGAGTCAATAAAAGA
* *
39087 GCTTAATTCAGGGTAATTAAGTGGAGTCAAT-AAAGA
1 ACTTAATTCAGGGTAATTAAGTCGAGTCAATAAAAGA
*
39123 ACTTAATTCAGGGTAATTAAGTCGAGTTAAT-AAAGA
1 ACTTAATTCAGGGTAATTAAGTCGAGTCAATAAAAGA
39159 ACTTAATTCAGGGTAATTAAGTCGAGTCAAT-AAAGA
1 ACTTAATTCAGGGTAATTAAGTCGAGTCAATAAAAGA
39195 ACTTAAT
1 ACTTAAT
39202 CTAAAAAGAG
Statistics
Matches: 140, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
35 4 0.03
36 136 0.97
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (37 bp):
ACTTAATTCAGGGTAATTAAGTCGAGTCAATAAAAGA
Found at i:58256 original size:33 final size:33
Alignment explanation
Indices: 58210--58287 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 33
58200 TGTTGTTTGC
* *
58210 GATGATACTAAATCTATTTTGGATGCTAATTGT
1 GATGAAACAAAATCTATTTTGGATGCTAATTGT
*
58243 GATGAAACAAAATCTGTTTTGGATGCTAATTGT
1 GATGAAACAAAATCTATTTTGGATGCTAATTGT
58276 GATGAAAACAAA
1 GATG-AAACAAA
58288 TATGTTTTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 34 0.83
34 7 0.17
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (33 bp):
GATGAAACAAAATCTATTTTGGATGCTAATTGT
Found at i:58294 original size:33 final size:33
Alignment explanation
Indices: 58226--58297 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
58216 ACTAAATCTA
*
58226 TTTTGGATGCTAATTGTGATGAAACAAAATCTG
1 TTTTGGATGCTAATTGTGATGAAACAAAATATG
58259 TTTTGGATGCTAATTGTGATGAAA-ACAAATATG
1 TTTTGGATGCTAATTGTGATGAAACA-AAATATG
58292 TTTTGG
1 TTTTGG
58298 TTGAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
32 1 0.03
33 36 0.97
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (33 bp):
TTTTGGATGCTAATTGTGATGAAACAAAATATG
Found at i:58800 original size:18 final size:19
Alignment explanation
Indices: 58777--58814 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
58767 GTGCATGGGC
*
58777 TGCATGGAG-GCATGGAGA
1 TGCATGGAGACCATGGAGA
58795 TGCATGGAGACCATGGAGA
1 TGCATGGAGACCATGGAGA
58814 T
1 T
58815 AACGATGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGGAGA
Found at i:59803 original size:48 final size:48
Alignment explanation
Indices: 59732--59827 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
59722 CTCCATTGTC
59732 ATTTTTGAGACACAAGTTGGATGTCTTCAAGTGCAAAAACTATTAGAA
1 ATTTTTGAGACACAAGTTGGATGTCTTCAAGTGCAAAAACTATTAGAA
* *
59780 ATTTTTGAGACCCAAGTTGGATGTCTTTAAGTGCAAAAACTATTAGAA
1 ATTTTTGAGACACAAGTTGGATGTCTTCAAGTGCAAAAACTATTAGAA
59828 CTTAAACCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (48 bp):
ATTTTTGAGACACAAGTTGGATGTCTTCAAGTGCAAAAACTATTAGAA
Found at i:64849 original size:2 final size:2
Alignment explanation
Indices: 64842--64870 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64832 CATTATGCCC
64842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64871 ATAAATTTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65098 original size:9 final size:9
Alignment explanation
Indices: 65084--65127 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
65074 GACCATTTGA
*
65084 ATAATATGT
1 ATAATATAT
65093 ATAATATAT
1 ATAATATAT
65102 AT--TATAT
1 ATAATATAT
65109 ATAATATAT
1 ATAATATAT
65118 AT-ATATAT
1 ATAATATAT
65126 AT
1 AT
65128 GATAGAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
7 7 0.22
8 8 0.25
9 17 0.53
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (9 bp):
ATAATATAT
Found at i:65103 original size:2 final size:2
Alignment explanation
Indices: 65087--65127 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
65077 CATTTGAATA
*
65087 AT AT GT AT A- AT AT AT AT -T AT AT AT A- 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
65126 AT
1 AT
65128 GATAGAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67547 original size:31 final size:31
Alignment explanation
Indices: 67512--67571 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
67502 GAGCATAACT
67512 TTTCCTACTCCTTTACATTACCAAACTGTAA
1 TTTCCTACTCCTTTACATTACCAAACTGTAA
*
67543 TTTCCTACTCCTTTACATTACCAAGCTGT
1 TTTCCTACTCCTTTACATTACCAAACTGT
67572 TACTACTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.40
Consensus pattern (31 bp):
TTTCCTACTCCTTTACATTACCAAACTGTAA
Found at i:68033 original size:16 final size:16
Alignment explanation
Indices: 68002--68040 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
67992 CACTCAAATG
68002 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
* *
68017 TTGGGTCAATTTTGGT
1 TCGGGTCAATTTGGGT
68033 TCGGGTCA
1 TCGGGTCA
68041 TATGATTCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.10, C:0.13, G:0.36, T:0.41
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:72064 original size:15 final size:15
Alignment explanation
Indices: 72044--72073 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
72034 TGCATCATAT
72044 GATAGATATTTTCTA
1 GATAGATATTTTCTA
72059 GATAGATATTTTCTA
1 GATAGATATTTTCTA
72074 TCTGAACCTT
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:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
GATAGATATTTTCTA
Found at i:72578 original size:16 final size:16
Alignment explanation
Indices: 72557--72595 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
72547 CCAACAAAAT
* *
72557 AAAAAATAAATAGAAA
1 AAAAAAGAAAAAGAAA
72573 AAAAAAGAAAAAGAAA
1 AAAAAAGAAAAAGAAA
72589 AAGAAAA
1 AA-AAAA
72596 AAGAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAA
Found at i:73912 original size:30 final size:30
Alignment explanation
Indices: 73875--73974 Score: 164
Period size: 30 Copynumber: 3.3 Consensus size: 30
73865 TTTCTCCTCG
* *
73875 ATCATCTCTATCCTGCCTTCTTTGATCTCT
1 ATCATCTCTGTCCTGCCTTCTTCGATCTCT
*
73905 GTCATCTCTGTCCTGCCTTCTTCGATCTCT
1 ATCATCTCTGTCCTGCCTTCTTCGATCTCT
73935 ATCATCTCTGTCCTGCCTTCTTCGATCTCT
1 ATCATCTCTGTCCTGCCTTCTTCGATCTCT
73965 ATCAGTCTCT
1 ATCA-TCTCT
73975 TCAGAAACAG
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 60 0.92
31 5 0.08
ACGTcount: A:0.11, C:0.35, G:0.10, T:0.44
Consensus pattern (30 bp):
ATCATCTCTGTCCTGCCTTCTTCGATCTCT
Found at i:78187 original size:16 final size:16
Alignment explanation
Indices: 78168--78242 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
78158 CCAAGATCCG
78168 AATGACCCGTAACTCA
1 AATGACCCGTAACTCA
* * *
78184 AATGACGCGAAACTCG
1 AATGACCCGTAACTCA
78200 AATGACCCGTAAC-C-
1 AATGACCCGTAACTCA
* * *
78214 CATGACCCGAAACGCA
1 AATGACCCGTAACTCA
*
78230 AATGACCCATAAC
1 AATGACCCGTAAC
78243 CCAAGATCCG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
14 11 0.23
15 2 0.04
16 34 0.72
ACGTcount: A:0.39, C:0.32, G:0.16, T:0.13
Consensus pattern (16 bp):
AATGACCCGTAACTCA
Found at i:78189 original size:32 final size:32
Alignment explanation
Indices: 78139--78246 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 32
78129 TGACCCAAAC
* *
78139 GACCCGCAACCCAGATGAC-CCAAGA-TCCGAAT
1 GACCCGTAACCCAAATGACGCCAA-ACT-CGAAT
* *
78171 GACCCGTAACTCAAATGACGCGAAACTCGAAT
1 GACCCGTAACCCAAATGACGCCAAACTCGAAT
* *
78203 GACCCGTAACCC--ATGAC-CCGAAACGCAAAT
1 GACCCGTAACCCAAATGACGCC-AAACTCGAAT
*
78233 GACCCATAACCCAA
1 GACCCGTAACCCAA
78247 GATCCGTATG
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
29 1 0.02
30 24 0.39
32 33 0.53
33 4 0.06
ACGTcount: A:0.37, C:0.35, G:0.17, T:0.11
Consensus pattern (32 bp):
GACCCGTAACCCAAATGACGCCAAACTCGAAT
Found at i:78225 original size:30 final size:30
Alignment explanation
Indices: 78166--78245 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
78156 ACCCAAGATC
* * *
78166 CGAATGACCCGTAACTCAAATGACGCGAAACT
1 CGAATGACCCGTAAC-C-CATGACCCGAAACG
78198 CGAATGACCCGTAACCCATGACCCGAAACG
1 CGAATGACCCGTAACCCATGACCCGAAACG
* *
78228 CAAATGACCCATAACCCA
1 CGAATGACCCGTAACCCA
78246 AGATCCGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 27 0.63
31 1 0.02
32 15 0.35
ACGTcount: A:0.38, C:0.34, G:0.16, T:0.12
Consensus pattern (30 bp):
CGAATGACCCGTAACCCATGACCCGAAACG
Found at i:78283 original size:22 final size:23
Alignment explanation
Indices: 78257--78301 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
78247 GATCCGTATG
*
78257 ACCCGAATAACTCGAGAA-ATTA
1 ACCCGAATAACCCGAGAATATTA
*
78279 ACCCGAATGACCCGAGAATATTA
1 ACCCGAATAACCCGAGAATATTA
78302 TAAACTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (23 bp):
ACCCGAATAACCCGAGAATATTA
Found at i:78854 original size:32 final size:32
Alignment explanation
Indices: 78818--78879 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
78808 CCAAAACCCG
* *
78818 AACCCGTCCAACCCGAGACCCGAATGACCCAA
1 AACCCGTACAACCCGAGACCCGAATAACCCAA
** *
78850 AACCCGTATGACCCGAGACTCGAATAACCC
1 AACCCGTACAACCCGAGACCCGAATAACCC
78880 GAATCCAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.34, C:0.40, G:0.16, T:0.10
Consensus pattern (32 bp):
AACCCGTACAACCCGAGACCCGAATAACCCAA
Found at i:78912 original size:16 final size:16
Alignment explanation
Indices: 78828--78909 Score: 67
Period size: 16 Copynumber: 5.2 Consensus size: 16
78818 AACCCGTCCA
*
78828 ACCCGAGACCCGAATG
1 ACCCGAAACCCGAATG
* *
78844 ACCCAAAACCCGTATG
1 ACCCGAAACCCGAATG
* * *
78860 ACCCGAGACTCGAATA
1 ACCCGAAACCCGAATG
* *
78876 ACCCGAATCCAG-ATG
1 ACCCGAAACCCGAATG
* *
78891 ATCTGAAACCCGAATG
1 ACCCGAAACCCGAATG
78907 ACC
1 ACC
78910 TGAGAAAACT
Statistics
Matches: 47, Mismatches: 18, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
15 10 0.21
16 37 0.79
ACGTcount: A:0.35, C:0.34, G:0.18, T:0.12
Consensus pattern (16 bp):
ACCCGAAACCCGAATG
Found at i:82083 original size:12 final size:12
Alignment explanation
Indices: 82066--82097 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
82056 TTGAAAATAA
82066 CAACTTAGTACC
1 CAACTTAGTACC
82078 CAACTTAGTACC
1 CAACTTAGTACC
82090 CAACTTAG
1 CAACTTAG
82098 CCCACAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.31, G:0.09, T:0.25
Consensus pattern (12 bp):
CAACTTAGTACC
Found at i:85187 original size:11 final size:11
Alignment explanation
Indices: 85171--85202 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
85161 GGAGTTCATG
85171 TTTGAAGATTA
1 TTTGAAGATTA
85182 TTTGAAGATTA
1 TTTGAAGATTA
85193 TTTGAAGATT
1 TTTGAAGATT
85203 TGAAGACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:94053 original size:16 final size:16
Alignment explanation
Indices: 94028--94060 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
94018 TGAGAGATAG
94028 AGCTAACCTATTTGTT
1 AGCTAACCTATTTGTT
*
94044 AGCTAGCCTATTTGTT
1 AGCTAACCTATTTGTT
94060 A
1 A
94061 TGGGGACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (16 bp):
AGCTAACCTATTTGTT
Found at i:96782 original size:9 final size:9
Alignment explanation
Indices: 96765--96797 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
96755 ATGTTGTGGC
*
96765 TTAAATAAG
1 TTAATTAAG
96774 TTAATTAAG
1 TTAATTAAG
96783 TTAATTAAG
1 TTAATTAAG
96792 TTAATT
1 TTAATT
96798 TGAGAGCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (9 bp):
TTAATTAAG
Found at i:99660 original size:11 final size:11
Alignment explanation
Indices: 99640--99670 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
99630 AAGATTTCAA
99640 CTGAAGATTAT
1 CTGAAGATTAT
*
99651 CTGGAGATTAT
1 CTGAAGATTAT
99662 CTGAAGATT
1 CTGAAGATT
99671 TAATAGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:102906 original size:88 final size:85
Alignment explanation
Indices: 102812--103061 Score: 304
Period size: 88 Copynumber: 2.8 Consensus size: 85
102802 AAAAAAGTGA
*
102812 TTTAAAATGATTTA-TCAAGAAAACAATGATTTCAAATAATTTACCAAAACAACAATGATTTTAA
1 TTTAAAATGATTTACT-AA-AAAACAATGATTTCAAATAATTTACTAAAA-AACAATGATTTTAA
*
102876 ATTATTTACTAAAAAAATACTAAT
63 ATAATTTACT-AAAAAATACTAAT
* * *
102900 TTTAAAATGATTTACTAAAAAGACAATGATTTCAAATTATTTACTAAAGAAAGAATGTTTTTAAA
1 TTTAAAATGATTTACTAAAAA-ACAATGATTTCAAATAATTTACTAAA-AAACAATGATTTTAAA
* * * **
102965 AAGATTTACTAAAATATAGTGGT
64 TA-ATTTACTAAAAAATACTAAT
* *
102988 TTTAAAATGATTTACTAAAAAACCAATGATTTCAAATGATTTACTAAAAAACAATGATTTAAAAA
1 TTTAAAATGATTTACTAAAAAA-CAATGATTTCAAATAATTTACTAAAAAACAATGATTT-TAAA
103053 TAATTTACT
64 TAATTTACT
103062 TTAAAAACAA
Statistics
Matches: 141, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
87 21 0.15
88 111 0.79
89 9 0.06
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.35
Consensus pattern (85 bp):
TTTAAAATGATTTACTAAAAAACAATGATTTCAAATAATTTACTAAAAAACAATGATTTTAAATA
ATTTACTAAAAAATACTAAT
Found at i:103089 original size:29 final size:28
Alignment explanation
Indices: 102787--103094 Score: 273
Period size: 29 Copynumber: 10.6 Consensus size: 28
102777 AAAGGAAAAA
102787 TCAAATGATTTA-TAAAAAA-AAGTGATT
1 TCAAATGATTTACTAAAAAACAA-TGATT
*
102814 TAAAATGATTTA-TCAAGAAAACAATGATT
1 TCAAATGATTTACT-AA-AAAACAATGATT
* *
102843 TCAAATAATTTACCAAAACAACAATGATT
1 TCAAATGATTTACTAAAA-AACAATGATT
* * *
102872 TTAAATTATTTACTAAAAAA-ATACTAATTT
1 TCAAATGATTTACTAAAAAACA-A-TGA-TT
*
102902 TAAAATGATTTACTAAAAAGACAATGATT
1 TCAAATGATTTACTAAAAA-ACAATGATT
* * *
102931 TCAAATTATTTACTAAAGAAAGAATGTTTT
1 TCAAATGATTTACTAAA-AAACAATG-ATT
* * * * * *
102961 TAAAAAGATTTACTAAAATATAGTGGTTT
1 TCAAATGATTTACTAAAAAACAAT-GATT
*
102990 TAAAATGATTTACTAAAAAACCAATGATT
1 TCAAATGATTTACTAAAAAA-CAATGATT
103019 TCAAATGATTTACTAAAAAACAATGATT
1 TCAAATGATTTACTAAAAAACAATGATT
* * *
103047 TAAAAATAATTTACTTTAAAAACAATGATT
1 T-CAAATGATTTAC-TAAAAAACAATGATT
*
103077 TCAATTGATTTACTAAAA
1 TCAAATGATTTACTAAAA
103095 GGTAGTGTTT
Statistics
Matches: 231, Mismatches: 34, Indels: 31
0.78 0.11 0.10
Matches are distributed among these distances:
27 13 0.06
28 20 0.09
29 136 0.59
30 59 0.26
31 2 0.01
32 1 0.00
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.35
Consensus pattern (28 bp):
TCAAATGATTTACTAAAAAACAATGATT
Found at i:103117 original size:58 final size:59
Alignment explanation
Indices: 102787--103138 Score: 235
Period size: 58 Copynumber: 6.0 Consensus size: 59
102777 AAAGGAAAAA
* * *
102787 TCAAATGATTTA-TAAAAAAAAGTGA-TTTAAAATGATTTA-TCAAGAAAA-CAATGATT
1 TCAAATGATTTACTAAAAAATAGTGATTTTAAAATAATTTACTTAA-AAAACCAATGATT
* * * * * * *
102843 TCAAATAATTTACCAAAACAACAATGATTTT-AAATTATTTACTAAAAAAATACTAAT--TT
1 TCAAATGATTTACTAAAA-AATAGTGATTTTAAAATAATTTACT-TAAAAA-ACCAATGATT
* * * * * * *
102902 TAAAATGATTTACTAAAAAGACAATGA-TTTCAAATTATTTAC-TAAAGAAA-GAATGTTTT
1 TCAAATGATTTACTAAAAA-ATAGTGATTTTAAAATAATTTACTTAAA-AAACCAATG-ATT
* * * * *
102961 TAAAAAGATTTACTAAAATATAGTGGTTTTAAAATGATTTAC-TAAAAAACCAATGATT
1 TCAAATGATTTACTAAAAAATAGTGATTTTAAAATAATTTACTTAAAAAACCAATGATT
* * * *
103019 TCAAATGATTTACTAAAAAACAATGATTTAAAAATAATTTACTTTAAAAA-CAATGATT
1 TCAAATGATTTACTAAAAAATAGTGATTTTAAAATAATTTACTTAAAAAACCAATGATT
* ** * * * *
103077 TCAATTGATTTACTAAAAGGTAGTGTTTTTCAAATTATTTA-TTGAAAAAAACCAAAGATT
1 TCAAATGATTTACTAAAAAATAGTGATTTTAAAATAATTTACTT--AAAAAACCAATGATT
103137 TC
1 TC
103139 GACCAATTCA
Statistics
Matches: 236, Mismatches: 41, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
56 14 0.06
57 10 0.04
58 104 0.44
59 93 0.39
60 12 0.05
61 3 0.01
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (59 bp):
TCAAATGATTTACTAAAAAATAGTGATTTTAAAATAATTTACTTAAAAAACCAATGATT
Found at i:106231 original size:68 final size:64
Alignment explanation
Indices: 106125--106268 Score: 225
Period size: 68 Copynumber: 2.2 Consensus size: 64
106115 CCTCGAATTA
*
106125 CTTTTACTTCTTGATCTTAATTGCTCTGAATTAAGTTAATTACTACTGGTTACTTCCTCTTACTC
1 CTTTTACTTCTTGATCTTAATTACTCTGAATTAAGTTAATTACTACTGGTTAC-TCCTCTTACTC
* *
106190 CTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGTTAATTACTACTGTTTACTCCTTTTAC
1 CTTTTACTTCTTGA-T--CTTAATTACTCTGAATTAAGTTAATTACTACTGGTTACTCCTCTTAC
106255 TC
63 TC
106257 CTTTTACTTCTT
1 CTTTTACTTCTT
106269 TTACTCCTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
65 14 0.19
66 1 0.01
67 22 0.30
68 36 0.49
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.50
Consensus pattern (64 bp):
CTTTTACTTCTTGATCTTAATTACTCTGAATTAAGTTAATTACTACTGGTTACTCCTCTTACTC
Found at i:106253 original size:9 final size:9
Alignment explanation
Indices: 106241--106282 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
106231 ATTACTACTG
106241 TTTACTCCT
1 TTTACTCCT
106250 TTTACTCCT
1 TTTACTCCT
*
106259 TTTACTTCT
1 TTTACTCCT
106268 TTTACTCCT
1 TTTACTCCT
106277 TTTACT
1 TTTACT
106283 TCTACTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTACTCCT
Found at i:106367 original size:53 final size:53
Alignment explanation
Indices: 106310--107054 Score: 1150
Period size: 53 Copynumber: 14.1 Consensus size: 53
106300 ATTACTTCTC
* * *
106310 TTACTGTTTAGGTGAATTACTCGGAATTAAACCTATTTACTAATTTTCTTCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
* * * *
106363 TTACTACTTAGGTTAATTACTCTGAATTAAACCTACTTACCAATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
*
106416 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACCAATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
*
106469 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTGATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
** * *
106522 TTACTATTTAGGTTAATTACTCTGAATTAAACCTATTTACTGATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
* * *
106575 TTACTGCTTAGGTTAATTATTCTGAATTAAACCTATTTACCAATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
*
106628 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTGATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
* * *
106681 TTACTGCCTAGGTTAATTACTCGGAATTAAATCTATTTACTGATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
* *
106734 TTAGTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTGATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
** ** *
106787 TTACTATTTAGGTTAATTACTCTAAATTAAACCTATTTACCAATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
* * *
106840 TTACTGCTTAGGTTAATTACTCGAAATTAAACCTATTTATTGATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
*
106893 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACCAATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
** * * *
106946 TTACTATTTAGGTTAATTACTCTGAATTAAACATATTTACTGATTTTCTCCTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
*
106999 TTACTGCTTAGGTTAATTACTCAGAATTAAACCTATTTACTAATTTTCT-CTT
1 TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
107051 TTAC
1 TTAC
107055 CTTTACCCTT
Statistics
Matches: 635, Mismatches: 57, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
52 7 0.01
53 628 0.99
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.46
Consensus pattern (53 bp):
TTACTGCTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTT
Found at i:112000 original size:10 final size:11
Alignment explanation
Indices: 111978--112010 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
111968 TAAGAGGTAA
111978 CTAAATCTTTT
1 CTAAATCTTTT
111989 CTAAAT-TTTT
1 CTAAATCTTTT
111999 CTAAATCTTTT
1 CTAAATCTTTT
112010 C
1 C
112011 ATTTATCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (11 bp):
CTAAATCTTTT
Found at i:112081 original size:13 final size:13
Alignment explanation
Indices: 112063--112105 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
112053 ATGAACATAT
*
112063 ATAAAAACTAGAA
1 ATAAAAAGTAGAA
112076 ATAAAAAGTAGAA
1 ATAAAAAGTAGAA
*
112089 ATATGAAAGTAGAA
1 ATA-AAAAGTAGAA
112103 ATA
1 ATA
112106 TGAGAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.65, C:0.02, G:0.14, T:0.19
Consensus pattern (13 bp):
ATAAAAAGTAGAA
Found at i:112097 original size:14 final size:14
Alignment explanation
Indices: 112071--112108 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
112061 ATATAAAAAC
*
112071 TAGAAATA-AAAAG
1 TAGAAATATGAAAG
112084 TAGAAATATGAAAG
1 TAGAAATATGAAAG
112098 TAGAAATATGA
1 TAGAAATATGA
112109 GAATATAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (14 bp):
TAGAAATATGAAAG
Found at i:116614 original size:47 final size:47
Alignment explanation
Indices: 116538--116630 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
116528 CCCAGCAGGA
* * *
116538 CCTTGATACTGCTGCATCTCTCTTAAAGGCCCAAAAGCACAC-AAGGG
1 CCTTGATACTGCTGAACCTCTCATAAAGGCCCAAAA-CACACGAAGGG
* *
116585 CCTTGTTACTGCTGAACCTCTCATGAAGGCCCAAAACACACGAAGG
1 CCTTGATACTGCTGAACCTCTCATAAAGGCCCAAAACACACGAAGG
116631 CCCAAACTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 5 0.12
47 35 0.88
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.20
Consensus pattern (47 bp):
CCTTGATACTGCTGAACCTCTCATAAAGGCCCAAAACACACGAAGGG
Found at i:126468 original size:63 final size:62
Alignment explanation
Indices: 126397--126637 Score: 277
Period size: 63 Copynumber: 4.0 Consensus size: 62
126387 AAAACTCTCG
* *
126397 AACAAGATTTTAGATTGAAAC-AGAAACTCTCGGCTAGAGACCTCGAGCAGGATTTGAAAACAA
1 AACAAGATTTTAGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTT-AAAA-AA
* * *
126460 AACAAGATTTTGGATTG-----A-AAACTCTCGACTAGAGACCTCGAGCAGGATTTAAAATGA
1 AACAAGATTTTAGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAA-AA
**
126517 AACAAGA-TTTAGATTGAAACAAGAAA--CTCGACTAGAGACCTCAAGCAGGATTTAAAATG
1 AACAAGATTTTAGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAAAA
** * *
126576 AACATTATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGTAGGATTTAAAAA
1 AACAAGATTTTAG-ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAAA
126638 TGAAACTCTC
Statistics
Matches: 155, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
56 8 0.05
57 12 0.08
58 31 0.20
59 6 0.04
60 34 0.22
61 15 0.10
62 3 0.02
63 46 0.30
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (62 bp):
AACAAGATTTTAGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAAAA
Found at i:126527 original size:17 final size:17
Alignment explanation
Indices: 126505--126540 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
126495 CCTCGAGCAG
126505 GATTTAAAATGAAACAA
1 GATTTAAAATGAAACAA
* *
126522 GATTTAGATTGAAACAA
1 GATTTAAAATGAAACAA
126539 GA
1 GA
126541 AACTCGACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.25
Consensus pattern (17 bp):
GATTTAAAATGAAACAA
Found at i:126674 original size:65 final size:61
Alignment explanation
Indices: 126477--126712 Score: 200
Period size: 65 Copynumber: 3.8 Consensus size: 61
126467 TTTTGGATTG
* **
126477 AAAACTCTCGACTAGAGACCTCGAGCAGGATTTAAAATGAAA---CAAGATTTAGATTGAAAC
1 AAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACTTCAAGA-GGA-ATTGAAAC
* ***
126537 AAGAA-ACTCGACTAGAGACCTCAAGCAGGATTTAAAATG-AACATT-ATTTTGGAATTGAAAC
1 AA-AACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAAC-TTCA-AGAGGAATTGAAAC
* *
126598 AAGAAACTCTCGACTAGAGACCTCAAGTAGGATTTAAAAATGAAACTCTCAAGCAGGATTTTGAA
1 -A-AAACTCTCGACTAGAGACCTCAAGCAGGATTT-AAAATGAAACT-TCAAG-AGGA-ATTGAA
126663 AC
60 AC
* *
126665 AAAACTCTCGAAC-AGAGACCTAAAACAGGATTTTAAAATGAAA-TTCAA
1 AAAACTCTCG-ACTAGAGACCTCAAGCAGGA-TTTAAAATGAAACTTCAA
126713 AGCAAAGAGA
Statistics
Matches: 143, Mismatches: 16, Indels: 31
0.75 0.08 0.16
Matches are distributed among these distances:
59 2 0.01
60 34 0.24
61 10 0.07
62 5 0.03
63 31 0.22
64 8 0.06
65 36 0.25
66 10 0.07
67 7 0.05
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (61 bp):
AAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACTTCAAGAGGAATTGAAAC
Found at i:126929 original size:33 final size:34
Alignment explanation
Indices: 126843--126933 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 34
126833 TTAAACGATG
*
126843 ATCCTAAACCAGGATTGAAATAACTCATAAAGCAATGA
1 ATCCTAAATCAGGATTG--A-AA-TCATAAAGCAATGA
* *
126881 A-CCTGAATCATGATTGAAATCATGAAA-CAAT-A
1 ATCCTAAATCAGGATTGAAATCAT-AAAGCAATGA
126913 ATCCTAAATCAGGATTGAAAT
1 ATCCTAAATCAGGATTGAAAT
126934 AAAGCCATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
32 2 0.04
33 25 0.54
34 5 0.11
35 1 0.02
37 12 0.26
38 1 0.02
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.24
Consensus pattern (34 bp):
ATCCTAAATCAGGATTGAAATCATAAAGCAATGA
Found at i:127111 original size:38 final size:37
Alignment explanation
Indices: 126970--127111 Score: 158
Period size: 38 Copynumber: 3.8 Consensus size: 37
126960 AACTGATTAA
* **
126970 AATGATCCTAAATCAAGATAAAAATGTATTAATAAATC
1 AATGATCCTAAATCAAGATTAAAATAAATT-ATAAATC
* * * *
127008 AATGATTCTAAACCAAGATTAAAATTAACTTATAAAGC
1 AATGATCCTAAATCAAGATTAAAA-TAAATTATAAATC
* * *
127046 AATGATCCTAGATCAGGATTAAGATAAATTGATAAATC
1 AATGATCCTAAATCAAGATTAAAATAAATT-ATAAATC
*
127084 AATGATCCTAAATCAGGATTAAAATAAA
1 AATGATCCTAAATCAAGATTAAAATAAA
127112 CCCACAAAGC
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
37 5 0.06
38 78 0.91
39 3 0.03
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (37 bp):
AATGATCCTAAATCAAGATTAAAATAAATTATAAATC
Found at i:127496 original size:168 final size:166
Alignment explanation
Indices: 127218--127674 Score: 682
Period size: 168 Copynumber: 2.7 Consensus size: 166
127208 AAATATGAAA
* *
127218 TGCCCGGAGGACTTATTAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACCA
1 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCT-AATTTGTGCCCGGAGGTCTTACCA
* * *
127283 ATGCAAACTCTTAATAGAGACCTTGACCAAGGATTTTAAACTTAAACACGAATTTTTGATGAAAA
65 ATGCAAACTCTTAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAATTTTT-ATG-AAA
* * *
127348 ACTTAAT-AAATGAAACGGTACCCGGAGGTTTTATCAAT
128 ACTCAATGAAATGAAACGGTACCCGAAGGTTTTACCAAT
* **
127386 TGCCCGGAGGACTTATCATAATTAATACTAGGAGGTTTCTAAGTTTGTGCCCGGAGGTCTTACCA
1 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTAA-TTTGTGCCCGGAGGTCTTACCA
127451 ATGCAAACTCTTAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAATCTTTTATGAAAA
65 ATGCAAACTCTTAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAAT-TTTTATGAAAA
* *
127516 CTCGATGAAATGAAATGGTACCCGAAGGTTTTACCAAT
129 CTCAATGAAATGAAACGGTACCCGAAGGTTTTACCAAT
* * ***
127554 TGCCCGGAGGACTTATCAGAATTAAAACCCGGAGGTTTCTAAATTTGTGCCCGGAGGACTTAATG
1 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCT-AATTTGTGCCCGGAGGTCTTACCA
*
127619 ATGCAAACTCTGAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAATTTT
65 ATGCAAACTCTTAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAATTTT
127675 AAACTTTAAC
Statistics
Matches: 263, Mismatches: 22, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
167 13 0.05
168 244 0.93
169 6 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (166 bp):
TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTAATTTGTGCCCGGAGGTCTTACCAA
TGCAAACTCTTAATAGAGACCTTTAACAAGGATTTTAAACTTAAACATGAATTTTTATGAAAACT
CAATGAAATGAAACGGTACCCGAAGGTTTTACCAAT
Found at i:127692 original size:19 final size:19
Alignment explanation
Indices: 127640--127693 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
127630 GAATAGAGAC
127640 CTTTAACAAGGATTTTAAA
1 CTTTAACAAGGATTTTAAA
* * *
127659 CTTAAACATGAATTTTAAA
1 CTTTAACAAGGATTTTAAA
127678 CTTTAACAAGGATTTT
1 CTTTAACAAGGATTTT
127694 TTATGAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (19 bp):
CTTTAACAAGGATTTTAAA
Found at i:128165 original size:36 final size:36
Alignment explanation
Indices: 128115--128241 Score: 200
Period size: 36 Copynumber: 3.5 Consensus size: 36
128105 ACTAAAGAAC
128115 GACCACCCTGGATCAACTAAAACGCATTGAAAAACT
1 GACCACCCTGGATCAACTAAAACGCATTGAAAAACT
*
128151 GACCACCCTAGATCAACTAAAACGCATTGAAAAACT
1 GACCACCCTGGATCAACTAAAACGCATTGAAAAACT
* * *
128187 GACCACCCTGGATCAATTAAAACGCATGGAAGAACT
1 GACCACCCTGGATCAACTAAAACGCATTGAAAAACT
*
128223 GGCCACCCTTGGATCAACT
1 GACCACCC-TGGATCAACT
128242 TGGAAACAAC
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 74 0.89
37 9 0.11
ACGTcount: A:0.39, C:0.28, G:0.16, T:0.17
Consensus pattern (36 bp):
GACCACCCTGGATCAACTAAAACGCATTGAAAAACT
Found at i:128510 original size:70 final size:70
Alignment explanation
Indices: 128231--128515 Score: 392
Period size: 70 Copynumber: 4.1 Consensus size: 70
128221 CTGGCCACCC
* * *
128231 TTGGATCAACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGATTGAATCGATCATTCTGACA
1 TTGGATCAACTTGGAAACAACTGAAGAAAGACTGCCCTAGGTCGACTGAATCGATCATTCTGACA
*
128296 TAAAG
66 TAAAT
* * *
128301 TTGGTTCAACTTGGAAACAACTGAAGAAAGACTGCCCTAGGTCGACTAAATCGATCATTTTGA-A
1 TTGGATCAACTTGGAAACAACTGAAGAAAGACTGCCCTAGGTCGACTGAATCGATCATTCTGACA
*
128365 TAAAAC
66 T-AAAT
* * *
128371 TTGGATAAACTTGGAAACAACTGACGAAAGACTGCCCTAGGTCGACTGACTCGATCATTCTGACA
1 TTGGATCAACTTGGAAACAACTGAAGAAAGACTGCCCTAGGTCGACTGAATCGATCATTCTGACA
128436 TAAAT
66 TAAAT
* * * * * *
128441 TTGGATCAACTTAGAAGCTACTAAAGAAAGACTGCCCTGGGTCGACTGAATCAATCATTCTGACA
1 TTGGATCAACTTGGAAACAACTGAAGAAAGACTGCCCTAGGTCGACTGAATCGATCATTCTGACA
128506 TAAAT
66 TAAAT
*
128511 CTGGA
1 TTGGA
128516 GAAAAACCAC
Statistics
Matches: 189, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
69 2 0.01
70 185 0.98
71 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (70 bp):
TTGGATCAACTTGGAAACAACTGAAGAAAGACTGCCCTAGGTCGACTGAATCGATCATTCTGACA
TAAAT
Found at i:128583 original size:49 final size:49
Alignment explanation
Indices: 128464--128610 Score: 206
Period size: 49 Copynumber: 3.0 Consensus size: 49
128454 GAAGCTACTA
** * *
128464 AAGAAAGACTGCCCTGGGTCGACTGAATCAATCATTCTGACATAAATCTG
1 AAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAA-CTG
* * *
128514 GAGAAAAACCACCCTGGGTCAACTGAATCGATTAGTT-TGACATAAACTG
1 AAGAAAGACCACCCTGGGTCAACTGAATCGATCA-TTCTGACATAAACTG
128563 AAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACT
1 AAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACT
128611 TGGATAAACT
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
48 2 0.02
49 45 0.53
50 36 0.42
51 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (49 bp):
AAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTG
Found at i:128672 original size:35 final size:35
Alignment explanation
Indices: 128633--128879 Score: 316
Period size: 35 Copynumber: 7.0 Consensus size: 35
128623 AAAACAATTG
*
128633 AAGAAAGACCTCCCTGGGTCAACTGAAATAAACTT
1 AAGAAAGACCGCCCTGGGTCAACTGAAATAAACTT
** * *
128668 AAGAAAGACTACCCTGGGTTAACTGAAATAAACTC
1 AAGAAAGACCGCCCTGGGTCAACTGAAATAAACTT
* *
128703 AAGAAAGACCGCCCTGGGTTAACTGAAATAAACTC
1 AAGAAAGACCGCCCTGGGTCAACTGAAATAAACTT
** * *
128738 AAGAAAGACCGCCCTAAGTTAACTGAAATAAACTC
1 AAGAAAGACCGCCCTGGGTCAACTGAAATAAACTT
128773 AAGAAAGACCGCCCTGGGTCAACTGAAATAAACTT
1 AAGAAAGACCGCCCTGGGTCAACTGAAATAAACTT
* * * *
128808 AAGAAAGATCGTCCTGGATCAACTGGAATAAA-TT
1 AAGAAAGACCGCCCTGGGTCAACTGAAATAAACTT
* *
128842 GAAGAAAGACCGCCCTGGGTCAACAAGAGATAAACTT
1 -AAGAAAGACCGCCCTGGGTCAAC-TGAAATAAACTT
128879 A
1 A
128880 TACTTTTGAA
Statistics
Matches: 187, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
34 2 0.01
35 176 0.94
36 7 0.04
37 2 0.01
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (35 bp):
AAGAAAGACCGCCCTGGGTCAACTGAAATAAACTT
Found at i:129996 original size:20 final size:20
Alignment explanation
Indices: 129967--130015 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
129957 TATCCTTTTC
129967 TCCTTCTTTTT-TTTTTCATT
1 TCCTT-TTTTTCTTTTTCATT
*
129987 TCCTTTTTTTCTTTTTCTTT
1 TCCTTTTTTTCTTTTTCATT
*
130007 TTCTTTTTT
1 TCCTTTTTT
130016 CCCTTTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (20 bp):
TCCTTTTTTTCTTTTTCATT
Found at i:130022 original size:20 final size:20
Alignment explanation
Indices: 129979--130022 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
129969 CTTCTTTTTT
* *
129979 TTTTCATTTCCTTTTTTTCT
1 TTTTCATTTCCTTTTTTCCC
* *
129999 TTTTCTTTTTCTTTTTTCCC
1 TTTTCATTTCCTTTTTTCCC
130019 TTTT
1 TTTT
130023 TAGCTTCACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCATTTCCTTTTTTCCC
Found at i:131193 original size:30 final size:30
Alignment explanation
Indices: 131157--131221 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
131147 AAGGGTCAAG
131157 TGGCCGGTTGTGGCCGGATGGCCCGTGCAA
1 TGGCCGGTTGTGGCCGGATGGCCCGTGCAA
* *
131187 TGGCCGGTTGTGGCCGGATGGCTCGTGCGA
1 TGGCCGGTTGTGGCCGGATGGCCCGTGCAA
131217 TGGCC
1 TGGCC
131222 CGTGCGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.08, C:0.26, G:0.45, T:0.22
Consensus pattern (30 bp):
TGGCCGGTTGTGGCCGGATGGCCCGTGCAA
Found at i:133149 original size:33 final size:33
Alignment explanation
Indices: 133107--133244 Score: 222
Period size: 33 Copynumber: 4.2 Consensus size: 33
133097 TTCTTTTCAC
* ** *
133107 CCAAAACAGAATTATTTTCAATATTATGTTCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
133140 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
133173 CCAAAATAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
133206 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
133239 TCAAAA
1 CCAAAA
133245 TAGATTTGTT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 98 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:133276 original size:66 final size:66
Alignment explanation
Indices: 133107--133281 Score: 199
Period size: 66 Copynumber: 2.7 Consensus size: 66
133097 TTCTTTTCAC
* * ** **
133107 CCAAAACAGAATTATTTTCAATATTATGTTCAACCAAAACAGAATTATTTGCAATGCTATGATCA
1 CCAAAATAGAATTATTTGCAATACCATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCA
133172 A
66 A
* * *
133173 CCAAAATAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
1 CCAAAATAGAATTATTTGCAATACCATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCA
133238 A
66 A
* * * * * *
133239 TCAAAATAGATTTGTTTTC-ATCACCATTAGCATCCAAAACAGA
1 CCAAAATAGAATTATTTGCAAT-ACCATGAGCAACCAAAACAGA
133282 TTTAGTATCA
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 2 0.02
66 92 0.98
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (66 bp):
CCAAAATAGAATTATTTGCAATACCATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCA
A
Found at i:135811 original size:30 final size:30
Alignment explanation
Indices: 135775--135839 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
135765 AAGGGTCAAG
* *
135775 TGGCCGGTTGTGGCCGGATGGCCCGTGCGA
1 TGGCCGGTTGTGACCGAATGGCCCGTGCGA
*
135805 TGGCCGGTTGTGACCGAATGGCTCGTGCGA
1 TGGCCGGTTGTGACCGAATGGCCCGTGCGA
135835 TGGCC
1 TGGCC
135840 CGTGCGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.09, C:0.26, G:0.43, T:0.22
Consensus pattern (30 bp):
TGGCCGGTTGTGACCGAATGGCCCGTGCGA
Found at i:136634 original size:19 final size:19
Alignment explanation
Indices: 136596--136635 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
136586 CCTAAAGAAT
** *
136596 AAGCCACGTGGCTTTTAAA
1 AAGCCACGTGGAATTAAAA
136615 AAGCCACGTGGAATTAAAA
1 AAGCCACGTGGAATTAAAA
136634 AA
1 AA
136636 TAAAGCAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (19 bp):
AAGCCACGTGGAATTAAAA
Found at i:138953 original size:8 final size:7
Alignment explanation
Indices: 138924--138983 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
138914 GAAAGATGAG
138924 AAAAAT-
1 AAAAATA
138930 AAAAAT-
1 AAAAATA
*
138936 GAAAATA
1 AAAAATA
138943 AAAATATA
1 AAAA-ATA
138951 AAAAATA
1 AAAAATA
*
138958 AAAAATT
1 AAAAATA
*
138965 AAAATTAA
1 AAAAAT-A
138973 AAAAATA
1 AAAAATA
138980 AAAA
1 AAAA
138984 GTGCCACATA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
6 11 0.24
7 22 0.49
8 12 0.27
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (7 bp):
AAAAATA
Found at i:138955 original size:15 final size:14
Alignment explanation
Indices: 138924--138983 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
138914 GAAAGATGAG
138924 AAAAAT-AAAAAT-
1 AAAAATAAAAAATA
*
138936 GAAAATAAAAATATA
1 AAAAATAAAAA-ATA
*
138951 AAAAATAAAAAATT
1 AAAAATAAAAAATA
*
138965 AAAATTAAAAAAATA
1 AAAAAT-AAAAAATA
138980 AAAA
1 AAAA
138984 GTGCCACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 5 0.13
13 4 0.10
14 9 0.23
15 21 0.54
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (14 bp):
AAAAATAAAAAATA
Found at i:138955 original size:22 final size:20
Alignment explanation
Indices: 138930--138983 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
138920 TGAGAAAAAT
*
138930 AAAAATGAAAATAAAAATATA
1 AAAAATAAAAATAAAAAT-TA
*
138951 AAAAATAAAAAATTAAAATTAA
1 AAAAAT-AAAAATAAAAATT-A
138973 AAAAATAAAAA
1 AAAAATAAAAA
138984 GTGCCACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAATAAAAATAAAAATTA
Found at i:139209 original size:13 final size:13
Alignment explanation
Indices: 139181--139237 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
139171 AAAAAGACTC
139181 AAAACC-TTTTTGG
1 AAAACCATTTTT-G
*
139194 AAACCCATTTTTG
1 AAAACCATTTTTG
*
139207 AAAACCTTTTATTG
1 AAAACCATTT-TTG
*
139221 AAAACAATTTTTG
1 AAAACCATTTTTG
139234 AAAA
1 AAAA
139238 ATGTATCTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 21 0.57
14 16 0.43
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (13 bp):
AAAACCATTTTTG
Found at i:139313 original size:11 final size:11
Alignment explanation
Indices: 139296--139331 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
139286 TTGGAACTTG
139296 ATTTTTCTTTT
1 ATTTTTCTTTT
*
139307 CTTTTTCTTTT
1 ATTTTTCTTTT
*
139318 ATTCTTCTTTT
1 ATTTTTCTTTT
139329 ATT
1 ATT
139332 CTTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (11 bp):
ATTTTTCTTTT
Found at i:139339 original size:11 final size:11
Alignment explanation
Indices: 139300--139338 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
139290 AACTTGATTT
* *
139300 TTCTTTTCTTT
1 TTCTTTTATTC
139311 TTCTTTTATTC
1 TTCTTTTATTC
139322 TTCTTTTATTC
1 TTCTTTTATTC
139333 TT-TTTT
1 TTCTTTT
139339 TTTAATCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 4 0.15
11 22 0.85
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTTATTC
Found at i:142379 original size:16 final size:17
Alignment explanation
Indices: 142355--142389 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
142345 TTTTCCATTT
*
142355 TTTTCTTTTTCTTTTCC
1 TTTTCTTTTTATTTTCC
142372 TTTT-TTTTTATTTTCC
1 TTTTCTTTTTATTTTCC
142388 TT
1 TT
142390 CAAATTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTCTTTTTATTTTCC
Found at i:143713 original size:20 final size:22
Alignment explanation
Indices: 143683--143723 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
143673 TTTTGTTTTT
*
143683 TTTTAAAAATTGATT-TTAAAA
1 TTTTAAAAATTAATTATTAAAA
143704 TTTT-AAAATTAATTATTAAA
1 TTTTAAAAATTAATTATTAAA
143724 TATACCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTAAAAATTAATTATTAAAA
Found at i:147645 original size:27 final size:26
Alignment explanation
Indices: 147573--147646 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 26
147563 AAGTGGACTC
*
147573 AAAATGACCAAAATGCCCCTGAATACA
1 AAAATGACCAAAATG-CCCTTAATACA
* * *
147600 AAAATGGCCAAAATGCCCTTAGTGCAA
1 AAAATGACCAAAATGCCCTTAATAC-A
147627 AAAATGACCAAAATGCCCTT
1 AAAATGACCAAAATGCCCTT
147647 GGATGACCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.18
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCTTAATACA
Found at i:150709 original size:27 final size:27
Alignment explanation
Indices: 150675--150746 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
150665 GGTCACATAG
150675 GGGCATTTTGGTCATTTTTGCA-CTAAA
1 GGGCATTTTGGTCATTTTTGCATC-AAA
* * * * *
150702 GGGTATTTGGGTCATTTGTGCATCCAT
1 GGGCATTTTGGTCATTTTTGCATCAAA
150729 GGGCATTTTGGTCATTTT
1 GGGCATTTTGGTCATTTT
150747 AAGTCCACTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTTGCATCAAA
Found at i:150979 original size:59 final size:59
Alignment explanation
Indices: 150887--151004 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
150877 GGTTTAACTT
150887 CATTTAGTTATTTAGTACTTGTTGCATTTTAAACACCTTTTAGAAATAGGCCTAGTTTG
1 CATTTAGTTATTTAGTACTTGTTGCATTTTAAACACCTTTTAGAAATAGGCCTAGTTTG
*
150946 CATTTAGTTATTTAGTACTTGTTGCATTTTAAACACCTTTTAGAAATAGGTCTAGTTTG
1 CATTTAGTTATTTAGTACTTGTTGCATTTTAAACACCTTTTAGAAATAGGCCTAGTTTG
151005 AAATTGGCAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (59 bp):
CATTTAGTTATTTAGTACTTGTTGCATTTTAAACACCTTTTAGAAATAGGCCTAGTTTG
Found at i:151932 original size:30 final size:30
Alignment explanation
Indices: 151896--151952 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
151886 TGAGAGGGTC
*
151896 AATGATGCGCCCAA-GGCTTATCATGGAAGG
1 AATGATGC-ACCAATGGCTTATCATGGAAGG
*
151926 AATGATGCACCAATGGCTTATTATGGA
1 AATGATGCACCAATGGCTTATCATGGA
151953 CTTGAAGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (30 bp):
AATGATGCACCAATGGCTTATCATGGAAGG
Found at i:160743 original size:30 final size:30
Alignment explanation
Indices: 160720--160783 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
160710 TCGCATATGT
*
160720 CCGGCCATTGGATGGAGCCATCGCACAAGA
1 CCGGCCATTGCATGGAGCCATCGCACAAGA
* *
160750 CCGGCCATTGCATGGAG-TAGCCGCACAAGA
1 CCGGCCATTGCATGGAGCCA-TCGCACAAGA
160780 CCGG
1 CCGG
160784 ACACATGGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.12
Consensus pattern (30 bp):
CCGGCCATTGCATGGAGCCATCGCACAAGA
Found at i:161956 original size:24 final size:24
Alignment explanation
Indices: 161907--161955 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
161897 TCAAAATTTG
161907 AAGGAAAATGAAAAAAGACAGGAA
1 AAGGAAAATGAAAAAAGACAGGAA
*
161931 AAGGAAAAATTAAAAAA-AC-GGAA
1 AAGG-AAAATGAAAAAAGACAGGAA
161954 AA
1 AA
161956 ATCAGAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 6 0.26
25 11 0.48
ACGTcount: A:0.69, C:0.04, G:0.20, T:0.06
Consensus pattern (24 bp):
AAGGAAAATGAAAAAAGACAGGAA
Found at i:165158 original size:33 final size:33
Alignment explanation
Indices: 165056--165143 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 33
165046 GTGTTTTAGA
*
165056 TGTTCTTTGCGATGATACTAAACCTAATTTGAG
1 TGTTCTTTGCAATGATACTAAACCTAATTTGAG
*
165089 TGTTGTTTGCAATGATACTAAACCTAATTTGAG
1 TGTTCTTTGCAATGATACTAAACCTAATTTGAG
*
165122 TGTTCTTTGCAATGAAACTAAA
1 TGTTCTTTGCAATGATACTAAA
165144 TCTGCTTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTTCTTTGCAATGATACTAAACCTAATTTGAG
Done.