Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold714
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: 120697
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:440 original size:12 final size:11
Alignment explanation
Indices: 425--454 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
415 TTTTTTCAAT
425 TTTTTTCTTTTC
1 TTTTTTC-TTTC
437 TTTTTTCTTTC
1 TTTTTTCTTTC
448 TTTTTTC
1 TTTTTTC
455 CTTGAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:1268 original size:3 final size:3
Alignment explanation
Indices: 1262--1294 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1252 AATAATAATA
1262 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1295 TAAAAAGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2758 original size:12 final size:11
Alignment explanation
Indices: 2738--2773 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
2728 AAATATAGAA
2738 AAACAAATAAT
1 AAACAAATAAT
2749 AAATCAAATAAT
1 AAA-CAAATAAT
2761 AAA-AAATAAT
1 AAACAAATAAT
2771 AAA
1 AAA
2774 GCTTAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
11 3 0.12
12 11 0.46
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (11 bp):
AAACAAATAAT
Found at i:3354 original size:15 final size:15
Alignment explanation
Indices: 3326--3354 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3316 AAAACCTAAA
3326 AGTTATCAAGTTTTT
1 AGTTATCAAGTTTTT
3341 AGTT-TCAAGTTTTT
1 AGTTATCAAGTTTTT
3355 CCAAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (15 bp):
AGTTATCAAGTTTTT
Found at i:5794 original size:13 final size:13
Alignment explanation
Indices: 5776--5801 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5766 ACGTTATGCT
5776 TTGTATCGATACA
1 TTGTATCGATACA
5789 TTGTATCGATACA
1 TTGTATCGATACA
5802 ATGAACATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5814 original size:19 final size:21
Alignment explanation
Indices: 5788--5840 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
5778 GTATCGATAC
5788 ATTGTATCGATACAATGAAC-
1 ATTGTATCGATACAATGAACA
*
5808 A-TGTATCGATAC-ATGGACA
1 ATTGTATCGATACAATGAACA
5827 ATTGTATCGATACA
1 ATTGTATCGATACA
5841 TGAGATTGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.17
19 12 0.41
20 12 0.41
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
ATTGTATCGATACAATGAACA
Found at i:5834 original size:20 final size:19
Alignment explanation
Indices: 5786--5843 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 19
5776 TTGTATCGAT
5786 ACATTGTATCGATACAATGA
1 ACATTGTATCGATAC-ATGA
*
5806 ACA-TGTATCGATACATGG
1 ACATTGTATCGATACATGA
5824 ACAATTGTATCGATACATGA
1 AC-ATTGTATCGATACATGA
5844 GATTGGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.15
19 12 0.35
20 17 0.50
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:12106 original size:13 final size:13
Alignment explanation
Indices: 12088--12114 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12078 ACAACATTCC
12088 TTGTATCGATACA
1 TTGTATCGATACA
12101 TTGTATCGATACA
1 TTGTATCGATACA
12114 T
1 T
12115 AGGGTACTAT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:14123 original size:14 final size:14
Alignment explanation
Indices: 14106--14139 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
14096 AAAACTTGAA
14106 AACTTTGATACCAG
1 AACTTTGATACCAG
*
14120 AACTTTGATACCGG
1 AACTTTGATACCAG
14134 AACTTT
1 AACTTT
14140 TCTAATGCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (14 bp):
AACTTTGATACCAG
Found at i:14667 original size:13 final size:13
Alignment explanation
Indices: 14649--14740 Score: 72
Period size: 13 Copynumber: 7.2 Consensus size: 13
14639 ACATTATGTT
14649 TTGTATCGATACA
1 TTGTATCGATACA
14662 TTGTATCGATACA
1 TTGTATCGATACA
*
14675 -TGTCGATACATGGTACA
1 TTGT--AT-C--GATACA
*
14692 ATGTATCGATACA
1 TTGTATCGATACA
14705 TTGTATCGATACA
1 TTGTATCGATACA
14718 -TG-AT-G--A-A
1 TTGTATCGATACA
14725 TTGTATCGATACA
1 TTGTATCGATACA
14738 TTG
1 TTG
14741 CTTGTAACGG
Statistics
Matches: 64, Mismatches: 3, Indels: 24
0.70 0.03 0.26
Matches are distributed among these distances:
7 1 0.02
8 3 0.05
9 2 0.03
10 2 0.03
11 2 0.03
12 6 0.09
13 34 0.53
14 2 0.03
15 2 0.03
16 2 0.03
17 5 0.08
18 3 0.05
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:14719 original size:33 final size:31
Alignment explanation
Indices: 14656--14740 Score: 111
Period size: 33 Copynumber: 2.7 Consensus size: 31
14646 GTTTTGTATC
14656 GATACATTGTATCGATACA-TGTCGATACAT
1 GATACATTGTATCGATACATTGTCGATACAT
* *
14686 GGTACAATGTATCGATACATTGTATCGATACAT
1 GATACATTGTATCGATACATTG--TCGATACAT
14719 GATGA-ATTGTATCGATACATTG
1 GAT-ACATTGTATCGATACATTG
14741 CTTGTAACGG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 17 0.36
31 2 0.04
33 27 0.57
34 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (31 bp):
GATACATTGTATCGATACATTGTCGATACAT
Found at i:17140 original size:23 final size:22
Alignment explanation
Indices: 17108--17156 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
17098 CTCGACTGTC
*
17108 AAACTCGATTGACC-AGAATGGTT
1 AAACTCGATTAACCGA-AAT-GTT
*
17131 AAACTTGATTAACCGAAATGTT
1 AAACTCGATTAACCGAAATGTT
17153 AAAC
1 AAAC
17157 CCTATTGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 15 0.65
24 1 0.04
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (22 bp):
AAACTCGATTAACCGAAATGTT
Found at i:18791 original size:13 final size:13
Alignment explanation
Indices: 18773--18798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18763 CATTTTGGGA
18773 TGTATCGATACAT
1 TGTATCGATACAT
18786 TGTATCGATACAT
1 TGTATCGATACAT
18799 CTTGTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:18795 original size:33 final size:32
Alignment explanation
Indices: 18753--18816 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
18743 TACAAGCCAA
*
18753 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
18786 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
18817 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:18905 original size:20 final size:21
Alignment explanation
Indices: 18858--18910 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
18848 GCCAATGACC
*
18858 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
18879 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
18899 TGTATCGATACA
1 TGTATCGATACA
18911 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:18916 original size:13 final size:13
Alignment explanation
Indices: 18898--18922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18888 ACATTTGGTC
18898 ATGTATCGATACA
1 ATGTATCGATACA
18911 ATGTATCGATAC
1 ATGTATCGATAC
18923 TATGCAATCT
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):
ATGTATCGATACA
Found at i:21397 original size:13 final size:13
Alignment explanation
Indices: 21379--21416 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
21369 ATAAACCCTT
21379 TGTATCGATACAC
1 TGTATCGATACAC
*
21392 TGTATCGATACAT
1 TGTATCGATACAC
21405 TGTATCGATACA
1 TGTATCGATACA
21417 GAGAATGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:21612 original size:8 final size:8
Alignment explanation
Indices: 21599--21624 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
21589 AACATCACTC
21599 ATCACAAA
1 ATCACAAA
21607 ATCACAAA
1 ATCACAAA
21615 ATCACAAA
1 ATCACAAA
21623 AT
1 AT
21625 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:27915 original size:52 final size:52
Alignment explanation
Indices: 27767--27895 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
27757 CGAAATATGA
27767 AAATTTTCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTTCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
27819 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTTCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
27871 AAATTTTCCTGCATGTATCGCTACA
1 AAATTTTCCTGCATGTATCGATACA
27896 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTTCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:27988 original size:13 final size:13
Alignment explanation
Indices: 27966--28055 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
27956 GGCAGTAGCT
*
27966 TTGTAGCGATACA
1 TTGTATCGATACA
27979 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
27995 CTTATGTATCGATACA
1 --T-TGTATCGATACA
28011 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
28027 CTTATGTATCGATACA
1 --T-TGTATCGATACA
28043 TTGTATCGATACA
1 TTGTATCGATACA
28056 ATACTTTATG
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 32 0.50
14 2 0.03
16 8 0.12
18 2 0.03
19 20 0.31
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:28004 original size:19 final size:18
Alignment explanation
Indices: 27980--28077 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
27970 AGCGATACAT
27980 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
27999 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
28012 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
28031 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
28044 TGTATCGATACAATACTTTA
1 TGTATCGATACAA-AC-TTA
28064 TGTATCGATACAAA
1 TGTATCGATACAAA
28078 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:28013 original size:32 final size:32
Alignment explanation
Indices: 27967--28075 Score: 182
Period size: 32 Copynumber: 3.4 Consensus size: 32
27957 GCAGTAGCTT
*
27967 TGTAGCGATACATTGTATCGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
*
27999 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
*
28031 TGTATCGATACATTGTATCGATACAATACTTTA
1 TGTATCGATACATTGTATCGATACAAAAC-TTA
28064 TGTATCGATACA
1 TGTATCGATACA
28076 AATCGTTGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 58 0.79
33 15 0.21
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAAAACTTA
Found at i:31271 original size:13 final size:13
Alignment explanation
Indices: 31253--31278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31243 CATTTTGGGA
31253 TGTATCGATACAT
1 TGTATCGATACAT
31266 TGTATCGATACAT
1 TGTATCGATACAT
31279 CTTGTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:31275 original size:33 final size:32
Alignment explanation
Indices: 31233--31296 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
31223 TACAAGCCAA
*
31233 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
31266 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
31297 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:32356 original size:25 final size:25
Alignment explanation
Indices: 32319--32368 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
32309 AATGGTATTG
*
32319 ATAAAGTTTAACTTTATCTAGGATT
1 ATAAAGTTCAACTTTATCTAGGATT
*
32344 ATAAAGTTCAACTTTATTTAGGATT
1 ATAAAGTTCAACTTTATCTAGGATT
32369 CTAGATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
ATAAAGTTCAACTTTATCTAGGATT
Found at i:36794 original size:26 final size:26
Alignment explanation
Indices: 36765--36819 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
36755 TAAAGATGGT
* * *
36765 ATTGATAAAGTTTAACTTTATTTGAG
1 ATTGATAAAATTCAACTTTATCTGAG
36791 ATTGATAAAATTCAACTTTATCTGAG
1 ATTGATAAAATTCAACTTTATCTGAG
36817 ATT
1 ATT
36820 CTAGATAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (26 bp):
ATTGATAAAATTCAACTTTATCTGAG
Found at i:39253 original size:32 final size:32
Alignment explanation
Indices: 39204--39278 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
39194 TGCAGATAAA
*
39204 ATAAT-TAAAATATTAATAT-TAAAAAATTTAT
1 ATAATATAAAATATTAATATAT-AAAAATATAT
* *
39235 ATAATATAAATTATTAATATATTAAAATATAT
1 ATAATATAAAATATTAATATATAAAAATATAT
39267 ATAAATATAAAA
1 AT-AATATAAAA
39279 ATTTTAACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 5 0.14
32 23 0.62
33 9 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAATATAAAATATTAATATATAAAAATATAT
Found at i:39259 original size:8 final size:8
Alignment explanation
Indices: 39200--39285 Score: 52
Period size: 8 Copynumber: 10.4 Consensus size: 8
39190 ATGATGCAGA
39200 TAAAATAAT
1 TAAAAT-AT
39209 TAAAATAT
1 TAAAATAT
39217 T--AATAT
1 TAAAATAT
*
39223 TAAAAAATT
1 TAAAATA-T
39232 TATATAATA-
1 TA-A-AATAT
*
39241 TAAATTAT
1 TAAAATAT
*
39249 TAATATAT
1 TAAAATAT
39257 TAAAATAT
1 TAAAATAT
39265 ATATAAATAT
1 -TA-AAATAT
* *
39275 AAAAATTT
1 TAAAATAT
39283 TAA
1 TAA
39286 CTATGATTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
6 6 0.10
7 3 0.05
8 27 0.45
9 14 0.23
10 7 0.12
11 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAAATAT
Found at i:39274 original size:18 final size:18
Alignment explanation
Indices: 39213--39280 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
39203 AATAATTAAA
* *
39213 ATATTAATATTAAAAAAT
1 ATATAAATATTAAAATAT
*
39231 TTATATAATA-T-AAAT-T
1 ATATA-AATATTAAAATAT
39247 AT-TAATATATTAAAATAT
1 ATATAA-ATATTAAAATAT
*
39265 ATATAAATATAAAAAT
1 ATATAAATATTAAAAT
39281 TTTAACTATG
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
14 1 0.03
15 5 0.13
16 3 0.08
17 7 0.18
18 16 0.41
19 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAAATATTAAAATAT
Found at i:40012 original size:22 final size:22
Alignment explanation
Indices: 39920--40012 Score: 57
Period size: 22 Copynumber: 4.3 Consensus size: 22
39910 TTCGAATAAG
* * *
39920 ATAATATGTATATCTAATAAAA
1 ATAATATGTACATATAGTAAAA
* *
39942 ATAATGTGTACATTTAGTAAAA
1 ATAATATGTACATATAGTAAAA
* * * *
39964 ACATTACGTACATACAGGT---A
1 ATAATATGTACATATA-GTAAAA
* *
39984 ATTATATGTATATATAGTAAAA
1 ATAATATGTACATATAGTAAAA
40006 ATAATAT
1 ATAATAT
40013 TTTTAACTTA
Statistics
Matches: 50, Mismatches: 17, Indels: 8
0.67 0.23 0.11
Matches are distributed among these distances:
19 2 0.04
20 11 0.22
22 35 0.70
23 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (22 bp):
ATAATATGTACATATAGTAAAA
Found at i:40081 original size:21 final size:21
Alignment explanation
Indices: 40066--40114 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
40056 TTTAAATAAG
40066 ATAATATATATATTAATAAAA
1 ATAATATATATATTAATAAAA
* *
40087 ATAATATGTATATTTAGTAAAA
1 ATAATATATATA-TTAATAAAA
*
40109 ACAATA
1 ATAATA
40115 CATACATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (21 bp):
ATAATATATATATTAATAAAA
Found at i:40220 original size:145 final size:145
Alignment explanation
Indices: 39914--40255 Score: 364
Period size: 146 Copynumber: 2.3 Consensus size: 145
39904 TATCCTTTCG
* * * * *
39914 AATAAGATAATATGTATATCTAATAAAAATAATGTGTACATTTAGTAAAAACATTACGTACATAC
1 AATAAGATAATATATATAT-TAATAAAAATAATATGTATATTTAGTAAAAACAATACATACATAC
* * * * * *
39979 AGGTAATTATATGTATATATAGTAAAAATAATATTTTTAACTTAAAGAGTTAGTTACTTTTATAA
65 AGATAACTATATGTACATATAGTAAAAATAATATTTTTAACTTAAAGAGTCAGGTACTTTCATAA
** *
40044 ATGGTTGATTCCTTTA
130 AAAGTCGATTCCTTTA
**
40060 AATAAGATAATATATATATTAATAAAAATAATATGTATATTTAGTAAAAACAATACATACATATT
1 AATAAGATAATATATATATTAATAAAAATAATATGTATATTTAGTAAAAACAATACATACATACA
* ** * ** * *
40125 GCATAACTATATGTGCATATAGTAAAAATGTTATTTTTAGCTTATGGTGTCAGGTCCTTTCATAG
66 G-ATAACTATATGTACATATAGTAAAAATAATATTTTTAACTTAAAGAGTCAGGTACTTTCATA-
* *
40190 AAAAGTCGATTCTTTTG
129 AAAAGTCGATTCCTTTA
* *
40207 AATAA-AGTAATATAAACATTCAATAAAAATAATATGTATAATTTA-TAAA
1 AATAAGA-TAATATATATATT-AATAAAAATAATATGTAT-ATTTAGTAAA
40256 TATAAAATGT
Statistics
Matches: 163, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
145 41 0.25
146 67 0.41
147 28 0.17
148 22 0.13
149 5 0.03
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (145 bp):
AATAAGATAATATATATATTAATAAAAATAATATGTATATTTAGTAAAAACAATACATACATACA
GATAACTATATGTACATATAGTAAAAATAATATTTTTAACTTAAAGAGTCAGGTACTTTCATAAA
AAGTCGATTCCTTTA
Found at i:40254 original size:22 final size:22
Alignment explanation
Indices: 40228--40283 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
40218 ATAAACATTC
40228 AATAAAAATAATATGTATAAT-T
1 AATAAAAATAATATGTA-AATAT
* * *
40250 TATAAATATAAAATGTAAATAT
1 AATAAAAATAATATGTAAATAT
*
40272 AATAAAAGTAAT
1 AATAAAAATAAT
40284 TTTTTTAGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (22 bp):
AATAAAAATAATATGTAAATAT
Found at i:40996 original size:26 final size:28
Alignment explanation
Indices: 40954--41014 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
40944 TTTATACATG
*
40954 ATATT-TTAATAATTTATA-AAT-TTAT
1 ATATTATTAATAAATTATATAATATTAT
40979 ATATTATTAATAAATTATATAATATTAT
1 ATATTATTAATAAATTATATAATATTAT
41007 -T-TTATTAA
1 ATATTATTAA
41015 AAGTAGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 5 0.16
26 19 0.59
27 4 0.12
28 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATATTATTAATAAATTATATAATATTAT
Found at i:40998 original size:18 final size:19
Alignment explanation
Indices: 40958--41005 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
40948 TACATGATAT
40958 TTTA-ATAAT-TT-ATAAA
1 TTTATATAATATTAATAAA
*
40974 TTTATATATTATTAATAAA
1 TTTATATAATATTAATAAA
40993 -TTATATAATATTA
1 TTTATATAATATTA
41006 TTTTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 4 0.15
18 14 0.52
19 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATATAATATTAATAAA
Found at i:41971 original size:24 final size:25
Alignment explanation
Indices: 41943--41996 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
41933 TATCAAACAC
*
41943 AATAAAAACACAATATAA-ATAAAT
1 AATAAAAACACAATATAACATAAAA
*
41967 AATAAAAACATAATATAACATAAAA
1 AATAAAAACACAATATAACATAAAA
41992 AATAA
1 AATAA
41997 TATTAATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (25 bp):
AATAAAAACACAATATAACATAAAA
Found at i:45287 original size:14 final size:14
Alignment explanation
Indices: 45268--45294 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45258 ATATATTTTG
45268 TTTTATTTAATTAA
1 TTTTATTTAATTAA
45282 TTTTATTTAATTA
1 TTTTATTTAATTA
45295 TACAAGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTTAATTAA
Found at i:50233 original size:20 final size:20
Alignment explanation
Indices: 50205--50279 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
50195 TTTTACCCAG
50205 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
50225 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
50245 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
50265 ATGTATCGATACATT
1 ATGTATCGATACATT
50280 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:50265 original size:40 final size:39
Alignment explanation
Indices: 50205--50282 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
50195 TTTTACCCAG
*
50205 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
50245 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
50283 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:63507 original size:13 final size:13
Alignment explanation
Indices: 63489--63577 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
63479 CATAAAGTGT
63489 TGTATCGATACAA
1 TGTATCGATACAA
63502 TGTATCGATACATAA
1 TGTATCGATAC--AA
63517 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
63534 TGTATCGATACATAA
1 TGTATCGATAC--AA
63549 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
63566 TGTATCGATACA
1 TGTATCGATACA
63578 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:63524 original size:32 final size:32
Alignment explanation
Indices: 63469--63598 Score: 242
Period size: 32 Copynumber: 4.0 Consensus size: 32
63459 TTCAACGATT
63469 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
63502 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
63534 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
63566 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
63598 T
1 T
63599 ATAAGCTACT
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 83 0.86
33 13 0.14
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:63526 original size:19 final size:18
Alignment explanation
Indices: 63467--63596 Score: 110
Period size: 19 Copynumber: 7.8 Consensus size: 18
63457 ATTTCAACGA
63467 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
63486 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
63502 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
63518 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
63534 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
63550 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
63566 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
63582 TTTTGTATCGATACA
1 -TTTGTATCGATACA
63597 ATATAAGCTA
Statistics
Matches: 92, Mismatches: 0, Indels: 38
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.36
15 6 0.07
17 6 0.07
19 35 0.38
20 12 0.13
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:63633 original size:64 final size:64
Alignment explanation
Indices: 63489--63633 Score: 179
Period size: 64 Copynumber: 2.3 Consensus size: 64
63479 CATAAAGTGT
* * ***
63489 TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATGTATCGATACATAAGTGT
1 TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATATATAGATACATAAGAAA
* *
63553 TGTATCGATACAATGTATCGATACATAAGTTTTGTATCGATACAATATA-AGCTAC-TGCCAAGA
1 TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATATATAGATACAT---AAGA
63616 AA
63 AA
63618 TGTATCGATAC-ATGTA
1 TGTATCGATACAATGTA
63634 AAATGTTGGA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
62 1 0.01
63 4 0.06
64 52 0.73
65 14 0.20
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (64 bp):
TGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAATATATAGATACATAAGAAA
Found at i:67441 original size:19 final size:19
Alignment explanation
Indices: 67417--67486 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
67407 CTTTACACCC
67417 AAAAAAAATAAAAAAACAA
1 AAAAAAAATAAAAAAACAA
* *
67436 AAAAAACAAAACAAAAAAAACA
1 AAAAAA-AATA-AAAAAACA-A
* *
67458 AAAAAAAACAAAAAAACCA
1 AAAAAAAATAAAAAAACAA
*
67477 AGAAAAAATA
1 AAAAAAAATA
67487 GCAAAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 15 0.37
20 9 0.22
21 10 0.24
22 7 0.17
ACGTcount: A:0.86, C:0.10, G:0.01, T:0.03
Consensus pattern (19 bp):
AAAAAAAATAAAAAAACAA
Found at i:67462 original size:32 final size:32
Alignment explanation
Indices: 67416--67495 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 32
67406 CCTTTACACC
*
67416 CAAAAAAAA-TAAAAAAACAAAAAAAACAAAA
1 CAAAAAAAACAAAAAAAACAAAAAAAACAAAA
* *
67447 CAAAAAAAACAAAAAAAAACAAAAAAACCAAGA
1 CAAAAAAAAC-AAAAAAAACAAAAAAAACAAAA
* *
67480 -AAAAATAGCAAAAAAA
1 CAAAAAAAACAAAAAAA
67496 GAAAAAGGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 16 0.38
32 7 0.17
33 19 0.45
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.03
Consensus pattern (32 bp):
CAAAAAAAACAAAAAAAACAAAAAAAACAAAA
Found at i:67482 original size:10 final size:9
Alignment explanation
Indices: 67416--67484 Score: 67
Period size: 9 Copynumber: 8.0 Consensus size: 9
67406 CCTTTACACC
67416 CAAAAAAAA
1 CAAAAAAAA
*
67425 -TAAAAAAA
1 CAAAAAAAA
67433 CAAAAAAAA
1 CAAAAAAAA
67442 C----AAAA
1 CAAAAAAAA
67447 CAAAAAAAA
1 CAAAAAAAA
67456 CAAAAAAAAA
1 C-AAAAAAAA
*
67466 CAAAAAAAC
1 CAAAAAAAA
67475 CAAGAAAAAA
1 CAA-AAAAAA
67485 TAGCAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
5 5 0.10
8 7 0.14
9 23 0.47
10 14 0.29
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.01
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:67493 original size:1 final size:1
Alignment explanation
Indices: 67417--67473 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
67407 CTTTACACCC
* * * * * *
67417 AAAAAAAATAAAAAAACAAAAAAAACAAAACAAAAAAAACAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
67474 CCAAGAAAAA
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:0.89, C:0.09, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:68839 original size:28 final size:28
Alignment explanation
Indices: 68709--69922 Score: 1403
Period size: 28 Copynumber: 42.6 Consensus size: 28
68699 GAATGTTCAT
*
68709 CCCTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
68737 CTTTTTTCAAAGCCCACGAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
68766 CCCTCTTCAAACCCCACAAGTCAGTGGCA
1 CCCT-TTCAAAGCCCACAAGTCAGTGGCA
*
68795 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
68824 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
68852 CTCTTTCAAAGCCCAGAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
68880 ACTTTTC-AAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
68907 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
68935 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
68963 CCCTTTCAGAGCCCACAAGTCAGTTGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
68991 TCATTTCAAAGCCCACGCAAGACAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
69021 CCCTTTTAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
69051 CCCTTTC-AAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
69078 CATTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
69106 CTCTTTTAAAGCCCACAATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
***
69134 TATTTTCAAAGCCCACACAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
* *
69164 CCCTTTGAAAGCCCACGCAAGTTAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* * *
69194 CCTTTTCAAAGCCCACGAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
69222 CCTTTTTCAAAGCCCACGAGTCAGTGGCA
1 CC-CTTTCAAAGCCCACAAGTCAGTGGCA
* *
69251 CTCTTTCAAAGCCTACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
69279 TCCTTTCAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
69309 CCCTTTTAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* * *
69339 CCTTTTCAAAGCCCACGAGTCTGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
69367 CTCTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
69395 CCCTTTC-AAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
69422 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
69450 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
69478 TCCTTTCAAAGCCCACGCAAGTCAGTGGTA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
69508 CCCTTTTAAAGCCCACACAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
** *
69538 CATTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
69566 CCTTTTTC-AAGCCCACAAGTCAGTGGCA
1 CC-CTTTCAAAGCCCACAAGTCAGTGGCA
** * * *
69594 CTTTTTTAAAGCCCACAAGTTAGAGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
69622 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
69650 CCTTTTCAAAGCCCACAAGTTAGTGACA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
69678 CACTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
69707 CCTTTTCAAAGCCCACAAGTCAATGAACA
1 CCCTTTCAAAGCCCACAAGTCAGTG-GCA
**
69736 CTTTTTC-AAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
69763 CTTTTTCAAAGCCCATAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
69791 TCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
69819 ACCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
69847 CATTTTCAAAGCCCACAAGTCAGTGACA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * **
69875 CTCTTTTCAAAGCTCACAAGCCAGTAGTAA
1 C-CCTTTCAAAGCCCACAAGTCAGT-GGCA
*
69905 CTCTTTTCAAAGCCCACA
1 C-CCTTTCAAAGCCCACA
69923 TGTGTCGGTG
Statistics
Matches: 1035, Mismatches: 125, Indels: 50
0.86 0.10 0.04
Matches are distributed among these distances:
27 79 0.08
28 576 0.56
29 171 0.17
30 205 0.20
31 2 0.00
32 2 0.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:69119 original size:199 final size:196
Alignment explanation
Indices: 68711--69922 Score: 1458
Period size: 199 Copynumber: 6.1 Consensus size: 196
68701 ATGTTCATCC
* * * *
68711 CTTTCAAAGCCCACGAGTCAGTGGCACTTTTTTCAAAGCCCACGAGTCAGTGGCACCCTCTTCAA
1 CTTTTAAAGCCCACAAGTCAGTGGCAC-ATTTTCAAAGCCCACAAGTCAGTGGCACCCT-TTCAA
*
68776 ACCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA
64 AGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA
*
68841 AGTCAGTGGCACTCTTTCAAAGCCCAGAAGTCAGTGGCA-ACTTTTC-AAGCCCACAAGTCAGTG
128 AGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACA-TTTTCAAAGCCCACAAGTCAGTG
68904 GCACT
192 GCACT
* ** *
68909 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAGAG
1 CTTTTAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * * *
68974 CCCACAAGTCAGTTGCATCATTTCAAAGCCCACGCAAGACAGTGGCACCCTTTTAAAGCCCACGC
66 CCCACAAGTCAGTGGCATCTTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCA--C
* * *
69039 AAGTCAGTGGCACCCTTTC-AAGCCCACGAGTCAGTGGCACATTTTCAAAGCCCACGAGTCAGTG
127 AAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTG
69103 GCACT
192 GCACT
* * *
69108 CTTTTAAAGCCCACAATTCAGTGGCATATTTTCAAAGCCCACACAAGTCAGTGGCACCCTTTGAA
1 CTTTTAAAGCCCACAAGTCAGTGGCACATTTTCAAAG-CC-CACAAGTCAGTGGCACCCTTTCAA
* * * * *
69173 AGCCCACGCAAGTTAGTGGCACCTTTTCAAAGCCCACGAGTTAGTGGCACCTTTTTCAAAGCCCA
64 AGCCCA--CAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACC-CTTTCAAAGCCCA
* * *
69238 CGAGTCAGTGGCACTCTTTCAAAGCCTACAAGTCAGTGGCATC-CTTTCAAAGCCCACGCAAGTC
126 CAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA-CATTTTCAAAGCCCA--CAAGTC
*
69302 AGTGGCACC
188 AGTGGCACT
* * * *
69311 CTTTTAAAGCCCACGCAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCTGTGGCACTCTTTCAA
1 CTTTTAAAGCCCA--CAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
* * * * * *
69376 AGCCCACGAGTCAGTGGCACCCTTTC-AAGCCCACGAGTCAGTGGCACCTTTTCAAAGCCCACGA
64 AGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA
*
69440 GTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACGCAAGTCAGT
129 GTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA-CATTTTCAAAGCCCA--CAAGTCAGT
* *
69504 GGTACC
191 GGCACT
* *
69510 CTTTTAAAGCCCACACAAGTCAGTGGCACATTTTCAAAGCCCACGAGTCAGTGGCACCTTTTTC-
1 CTTTTAAAG-CC-CACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACC-CTTTCA
* * * *
69574 AAGCCCACAAGTCAGTGGCA-CTTTTTTAAAGCCCACAAGTTAGAGGCATCCTTTCAAAGCCCAC
63 AAGCCCACAAGTCAGTGGCATC-TTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
* *
69638 AAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTTAGTGACACACTTTTCAAAGCCCACAAGTCAG
127 AAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACA-TTTTCAAAGCCCACAAGTCAG
69702 TGGCAC-
190 TGGCACT
* * * **
69708 CTTTTCAAAGCCCACAAGTCAATGAACACTTTTTC-AAGCCCACAAGTCAGTGGCACTTTTTCAA
1 CTTTT-AAAGCCCACAAGTCAGTG-GCACATTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
* * * *
69772 AGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAA
64 AGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA
* * * *
69837 GTCAGTGGCACAT-TTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAGCTCACAAGCCAGTA
129 GTCAGTGGCAC-TCTTTCAAAGCCCACAAGTCAGTGGCAC-ATTTTCAAAGCCCACAAGTCAGT-
**
69901 GTAACT
191 GGCACT
69907 CTTTTCAAAGCCCACA
1 CTTTT-AAAGCCCACA
69923 TGTGTCGGTG
Statistics
Matches: 897, Mismatches: 83, Indels: 67
0.86 0.08 0.06
Matches are distributed among these distances:
195 14 0.02
196 26 0.03
197 200 0.22
198 69 0.08
199 263 0.29
200 113 0.13
201 101 0.11
202 12 0.01
203 76 0.08
204 2 0.00
205 21 0.02
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (196 bp):
CTTTTAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
CCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
CAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCAC
T
Found at i:70557 original size:20 final size:20
Alignment explanation
Indices: 70529--70603 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
70519 TTTTACCTAG
70529 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
70549 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
70569 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
*
70589 ATGTATTGATACATT
1 ATGTATCGATACATT
70604 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:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:70589 original size:40 final size:39
Alignment explanation
Indices: 70529--70606 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
70519 TTTTACCTAG
*
70529 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* * *
70569 ATGTATCGATATATTCTTCAATGTATTGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
70607 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:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:76731 original size:2 final size:2
Alignment explanation
Indices: 76724--76761 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
76714 GTGGTGTTTT
76724 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
76762 ATTTTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77378 original size:3 final size:3
Alignment explanation
Indices: 77370--77402 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
77360 AGGGGAAAAC
77370 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
77403 GGCTTTGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:77792 original size:2 final size:2
Alignment explanation
Indices: 77785--77815 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
77775 ATTTGAATTT
77785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
77816 TAATGAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78162 original size:3 final size:3
Alignment explanation
Indices: 78154--78181 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
78144 ATTAGCAAAT
78154 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
78182 ATGTAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:78703 original size:21 final size:20
Alignment explanation
Indices: 78673--78713 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
78663 ATTAAAAAAT
78673 TATTTTTAT-ATTAATATTTA
1 TATTTTTATAATTAA-ATTTA
78693 TATTATTTATAATTAAATTTA
1 TATT-TTTATAATTAAATTTA
78714 AATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTTATAATTAAATTTA
Found at i:83767 original size:63 final size:62
Alignment explanation
Indices: 83647--83768 Score: 142
Period size: 63 Copynumber: 2.0 Consensus size: 62
83637 GTTGAGCTAG
* * *
83647 ATTAAAATTTTTAAAATTTTTTATTTAAATTTAAAAATATTAATTTTATTATATATTATATT
1 ATTAAAATATTTAAAATTTTTTATTAAAATTTAAAAATAATAATTTTATTATATATTATATT
* *
83709 ATTAAAATATTTATATATTTTTTATAATAAAATTTAAATAA-AAT-ATTTTATT-TTTATTAT
1 ATTAAAATATTTA-AAATTTTTTAT--TAAAATTTAAA-AATAATAATTTTATTATATATTAT
83769 TAAATAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
62 12 0.24
63 17 0.33
64 8 0.16
65 12 0.24
66 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (62 bp):
ATTAAAATATTTAAAATTTTTTATTAAAATTTAAAAATAATAATTTTATTATATATTATATT
Found at i:94944 original size:55 final size:55
Alignment explanation
Indices: 94879--94990 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
94869 TTCAAACTTC
94879 TGAATTACAGTTCCCAAAAGGGGATAGCTGTTTCAGAATAAATATTCCACTTTGT
1 TGAATTACAGTTCCCAAAAGGGGATAGCTGTTTCAGAATAAATATTCCACTTTGT
94934 TGAATTACAGTTCCCAAAAGGGGATAGCTGTTTCAGAATAAATATTCCACTTTGT
1 TGAATTACAGTTCCCAAAAGGGGATAGCTGTTTCAGAATAAATATTCCACTTTGT
94989 TG
1 TG
94991 GAGCATAGAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (55 bp):
TGAATTACAGTTCCCAAAAGGGGATAGCTGTTTCAGAATAAATATTCCACTTTGT
Found at i:96907 original size:36 final size:37
Alignment explanation
Indices: 96848--96918 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
96838 TATTATTTTT
*
96848 TTAATTTTTTATTTAAATATTATAATTTATT-TTATAA
1 TTAATTTTTTATTAAAATATTATAA-TTATTCTTATAA
96885 TTAATTTTATT-TTAAAAT-TTATAATTATTCTTAT
1 TTAATTTT-TTATTAAAATATTATAATTATTCTTAT
96919 TCAAAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
35 5 0.16
36 10 0.32
37 14 0.45
38 2 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (37 bp):
TTAATTTTTTATTAAAATATTATAATTATTCTTATAA
Found at i:96925 original size:24 final size:24
Alignment explanation
Indices: 96878--96926 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
96868 TATAATTTAT
**
96878 TTTATAATTAATTTTATTTTAAAA
1 TTTATAATTAATTTTATTCAAAAA
96902 TTTATAATT-ATTCTTATTCAAAAA
1 TTTATAATTAATT-TTATTCAAAAA
96926 T
1 T
96927 ATTAACTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTATAATTAATTTTATTCAAAAA
Found at i:97349 original size:32 final size:33
Alignment explanation
Indices: 97284--97354 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
97274 GTTAAAACAG
* * *
97284 ATATAATATGAATATAAAAATATCTTAATATTT
1 ATATAATACGAATATAAAAATATATTAAAATTT
**
97317 ATATAATACGAAT-TATTAATATATTAAAATTT
1 ATATAATACGAATATAAAAATATATTAAAATTT
97349 ATATAA
1 ATATAA
97355 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (33 bp):
ATATAATACGAATATAAAAATATATTAAAATTT
Found at i:110769 original size:13 final size:13
Alignment explanation
Indices: 110751--110776 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
110741 CATTTTGGAA
110751 TGTATCGATACAT
1 TGTATCGATACAT
110764 TGTATCGATACAT
1 TGTATCGATACAT
110777 CTTGTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:110773 original size:33 final size:32
Alignment explanation
Indices: 110731--110794 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
110721 TACAAGCCAA
*
110731 TGTATCGATACATTTTG-GAATGTATCGATACAT
1 TGTATCGATACATCTTGTG--TGTATCGATACAT
110764 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGTGTGTATCGATACA
110795 AACAGTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 16 0.55
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGTGTGTATCGATACAT
Found at i:110882 original size:13 final size:13
Alignment explanation
Indices: 110864--110888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
110854 ACATTTGGTC
110864 ATGTATCGATACA
1 ATGTATCGATACA
110877 ATGTATCGATAC
1 ATGTATCGATAC
110889 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:112892 original size:21 final size:22
Alignment explanation
Indices: 112868--112912 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
112858 GTGTGGGGGC
*
112868 TGCCCGATTGCGACCTGG-GAG
1 TGCCCGATCGCGACCTGGTGAG
*
112889 TG-CCGGTCGCGACCTGGTGAG
1 TGCCCGATCGCGACCTGGTGAG
112910 TGC
1 TGC
112913 TGCCTAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.11, C:0.29, G:0.40, T:0.20
Consensus pattern (22 bp):
TGCCCGATCGCGACCTGGTGAG
Done.