Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2627
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: 74368
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:2635 original size:28 final size:29
Alignment explanation
Indices: 2599--2680 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
2589 AATTTTCACA
*
2599 ATCGAGGATACTCCAACCTCGTTATTTC-
1 ATCGGGGATACTCCAACCTCGTTATTTCG
*
2627 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCTCGTTA-TTTCG
* * *
2657 A--AGGAACACTCCAACCTCGTTATT
1 ATCGGGGATACTCCAACCTCGTTATT
2681 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 2 0.04
28 39 0.85
29 4 0.09
30 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCTCGTTATTTCG
Found at i:3693 original size:18 final size:18
Alignment explanation
Indices: 3658--3695 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3648 TAATTAATTG
3658 TCAACTTTATAAATTTTT
1 TCAACTTTATAAATTTTT
3676 TCAA-TTTATTAATATTTTT
1 TCAACTTTA-TAA-ATTTTT
3695 T
1 T
3696 TGATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 7 0.39
19 7 0.39
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (18 bp):
TCAACTTTATAAATTTTT
Found at i:4260 original size:13 final size:13
Alignment explanation
Indices: 4244--4282 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
4234 TAAAAGCTTA
4244 TTTTTC-TTTTCT
1 TTTTTCTTTTTCT
4256 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
4269 TTTCTT-TTTTTCT
1 TTT-TTCTTTTTCT
4282 T
1 T
4283 CTATTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.24
13 17 0.68
14 2 0.08
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:4267 original size:18 final size:18
Alignment explanation
Indices: 4244--4278 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4234 TAAAAGCTTA
4244 TTTTTCTTTTCTTTTTTC
1 TTTTTCTTTTCTTTTTTC
4262 TTTTTCTTTTCTTTTTT
1 TTTTTCTTTTCTTTTTT
4279 TCTTCTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTTTC
Found at i:5674 original size:36 final size:37
Alignment explanation
Indices: 5619--5692 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
5609 GTAAATTTAG
* * *
5619 ATTTTATTTAATTTGTAATAACAAACAT-TAAAGAAA
1 ATTTTATTTAACTTATAATAACAAACATAAAAAGAAA
*
5655 ATTTTATTTAACTTATAATAATAAACATAAAAAGAAA
1 ATTTTATTTAACTTATAATAACAAACATAAAAAGAAA
5692 A
1 A
5693 AAAAGTTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 25 0.76
37 8 0.24
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.36
Consensus pattern (37 bp):
ATTTTATTTAACTTATAATAACAAACATAAAAAGAAA
Found at i:11118 original size:26 final size:27
Alignment explanation
Indices: 11088--11139 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
11078 TTAATTTTGG
*
11088 TTGAAA-AACGGGATTAGAGTGTCTCC
1 TTGAAAGAACGGGATTAGAGTATCTCC
* *
11114 TTGAAAGAATGGGGTTAGAGTATCTC
1 TTGAAAGAACGGGATTAGAGTATCTC
11140 TGATGACGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.29
Consensus pattern (27 bp):
TTGAAAGAACGGGATTAGAGTATCTCC
Found at i:13651 original size:52 final size:50
Alignment explanation
Indices: 13594--13730 Score: 163
Period size: 52 Copynumber: 2.7 Consensus size: 50
13584 ATTTAACTGG
13594 ATGTATCGATACATGAAAGAATGTATCGATACATTTGGGTAAAAAACCCAAA
1 ATGTATCGATACATGAAAGAATGTATCGATACATTT-GG-AAAAAACCCAAA
* * ** *
13646 ATGTATAGATACAATG-AAGAATGTATCAATACATTTGGATCAAACCCAGA
1 ATGTATCGATAC-ATGAAAGAATGTATCGATACATTTGGAAAAAACCCAAA
*
13696 ATGTATCGATATAAT-AAA-AATGTATCGATACATTT
1 ATGTATCGATA-CATGAAAGAATGTATCGATACATTT
13731 TCTTTTCAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
49 16 0.22
50 23 0.31
51 2 0.03
52 30 0.41
53 3 0.04
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (50 bp):
ATGTATCGATACATGAAAGAATGTATCGATACATTTGGAAAAAACCCAAA
Found at i:13805 original size:20 final size:20
Alignment explanation
Indices: 13768--13818 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
13758 ATAAAGTCTA
* *
13768 GTATCGATACATTTACTTAT
1 GTATCGATATATTCACTTAT
*
13788 GTATCAATATATTCACTTAT
1 GTATCGATATATTCACTTAT
13808 GTATCGATATA
1 GTATCGATATA
13819 ACAAGTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (20 bp):
GTATCGATATATTCACTTAT
Found at i:15210 original size:21 final size:22
Alignment explanation
Indices: 15170--15210 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
15160 TCAAACCATC
* *
15170 ATATTTATAAAGTTGAAATTGG
1 ATATTTATAAACTAGAAATTGG
15192 ATATTTA-AAACTAGAAATT
1 ATATTTATAAACTAGAAATT
15211 AATTTAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (22 bp):
ATATTTATAAACTAGAAATTGG
Found at i:16205 original size:22 final size:22
Alignment explanation
Indices: 16180--16232 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
16170 AAAGCTTGTG
*
16180 ATATAATTTACTTTTTGATAAA
1 ATATAATTTACTTTTTAATAAA
16202 ATATAATTTACTTTTTAATAAA
1 ATATAATTTACTTTTTAATAAA
* *
16224 TTATTATTT
1 ATATAATTT
16233 CATCATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATAATTTACTTTTTAATAAA
Found at i:17368 original size:30 final size:30
Alignment explanation
Indices: 17251--17369 Score: 107
Period size: 30 Copynumber: 4.0 Consensus size: 30
17241 ATGTTAAATA
* * * *
17251 AAATATTAATTTAAG-TAAAAGCTTTATTT
1 AAATATAAATTAAAGATTAAAGATTTATTT
** * * *
17280 AGTTACAAATTAAATATTAAA-ATTTTATTC
1 AAATATAAATTAAAGATTAAAGA-TTTATTT
* * *
17310 GAATAAAAATTAAAGATTAAAGACTTATTT
1 AAATATAAATTAAAGATTAAAGATTTATTT
17340 AAATATAAATTAAAGATTAAAGATTTATTT
1 AAATATAAATTAAAGATTAAAGATTTATTT
17370 TAGTCTAATA
Statistics
Matches: 68, Mismatches: 19, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
29 9 0.13
30 58 0.85
31 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (30 bp):
AAATATAAATTAAAGATTAAAGATTTATTT
Found at i:17400 original size:20 final size:20
Alignment explanation
Indices: 17375--17413 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17365 TATTTTAGTC
17375 TAATAAAAATATAAAATTTT
1 TAATAAAAATATAAAATTTT
*
17395 TAATAAAATTATAAAATTT
1 TAATAAAAATATAAAATTT
17414 AAAAGCTTTT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATAAAAATATAAAATTTT
Found at i:17719 original size:3 final size:3
Alignment explanation
Indices: 17711--17740 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17701 ATATCAATTC
17711 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17741 GTAATAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17820 original size:14 final size:16
Alignment explanation
Indices: 17792--17825 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
17782 CAAAGTAGAT
17792 AAAAATAGTATTTTTA
1 AAAAATAGTATTTTTA
17808 AAAAATA-TA-TTTTA
1 AAAAATAGTATTTTTA
17822 AAAA
1 AAAA
17826 GAATATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 2 0.11
16 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAAATAGTATTTTTA
Found at i:17830 original size:16 final size:15
Alignment explanation
Indices: 17792--17831 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
17782 CAAAGTAGAT
*
17792 AAAAATAGTATTTTTA
1 AAAAATA-TATTTTAA
17808 AAAAATATATTTTAA
1 AAAAATATATTTTAA
17823 AAAGAATAT
1 AAA-AATAT
17832 TAAGTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
AAAAATATATTTTAA
Found at i:31948 original size:4 final size:4
Alignment explanation
Indices: 31939--31984 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
31929 TCTGTGAAAG
** *
31939 CATA CATA CATA CATA CATA CATA TGTG CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
31985 CTTGCACAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:34534 original size:166 final size:171
Alignment explanation
Indices: 34236--34572 Score: 443
Period size: 166 Copynumber: 2.0 Consensus size: 171
34226 TGATGGGACT
* * *
34236 TTCTGGAGTCGTTGGATAAAACCAGATGCCATTGCCCAAGCCGAAGTATGATCTTTATATATATA
1 TTCTGGAGTCGATGGATAAAACCAGATGCCATTGCCCAAGCCGAACTATGATC--TATAGATATA
* * *
34301 TATATTTTTTACCAATCTTATTCTATCCAAGGTTTCTTGAATGTTGGTTGTACATGTTTAAGTTC
64 TATATTTTTTACCAATCTTATTCTATCCAAAGTTTCTTGAATGTTAGTTATACATGTTTAAGTTC
* *
34366 TATGTTCATATAAGACAATTAATT-GATCCATCTGGCTAAGCA
129 TATCTTCATATAAGACAATTAATTGGATCCATCTGCCTAAGCA
* * *
34408 TTCTGGAGTCGATGGATAAAACCAGATGTCATTGCCTAAGCTGAACTATGATC-AT-GATATAT-
1 TTCTGGAGTCGATGGATAAAACCAGATGCCATTGCCCAAGCCGAACTATGATCTATAGATATATA
* * * *
34470 T-TTTTTTATCAATCTTATTCTA-CCAAAAGTTTCTTGATTGTTAGTTATAGATTTTTAAGTTCT
66 TATTTTTTACCAATCTTATTCTATCC-AAAGTTTCTTGAATGTTAGTTATACATGTTTAAGTTCT
* * *
34533 ATCTTCATATTAGACAATTAGTTGGATCCATTTGCCTAAG
130 ATCTTCATATAAGACAATTAATTGGATCCATCTGCCTAAG
34573 TTATTTTTCT
Statistics
Matches: 145, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
165 2 0.01
166 72 0.50
167 15 0.10
168 6 0.04
169 2 0.01
172 48 0.33
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (171 bp):
TTCTGGAGTCGATGGATAAAACCAGATGCCATTGCCCAAGCCGAACTATGATCTATAGATATATA
TATTTTTTACCAATCTTATTCTATCCAAAGTTTCTTGAATGTTAGTTATACATGTTTAAGTTCTA
TCTTCATATAAGACAATTAATTGGATCCATCTGCCTAAGCA
Found at i:39787 original size:6 final size:6
Alignment explanation
Indices: 39776--39826 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
39766 ATTAAAATTT
* * *
39776 ATATAA ATATAA ATATTTAA ATATAT ATATAT ATATAT ATATAA ATATAA
1 ATATAA ATATAA ATA--TAA ATATAA ATATAA ATATAA ATATAA ATATAA
39826 A
1 A
39827 GTTTGAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 35 0.85
8 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
ATATAA
Found at i:39792 original size:24 final size:24
Alignment explanation
Indices: 39764--39824 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
39754 TTCTAAATTT
*
39764 ATATTAAAATTTATATAAATATAA
1 ATATTAAAATATATATAAATATAA
* * *
39788 ATATTTAAATATATATATATATAT
1 ATATTAAAATATATATAAATATAA
39812 ATA-TATAAATATA
1 ATATTA-AAATATA
39825 AAGTTTGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATTAAAATATATATAAATATAA
Found at i:39796 original size:8 final size:8
Alignment explanation
Indices: 39782--39824 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
39772 ATTTATATAA
39782 ATATAAAT
1 ATATAAAT
*
39790 ATTTAAAT
1 ATATAAAT
*
39798 ATATATAT
1 ATATAAAT
*
39806 ATATATAT
1 ATATAAAT
39814 ATATAAAT
1 ATATAAAT
39822 ATA
1 ATA
39825 AAGTTTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
ATATAAAT
Found at i:39813 original size:14 final size:14
Alignment explanation
Indices: 39775--39818 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
39765 TATTAAAATT
*
39775 TATATAAATATAAA
1 TATATAAATATATA
*
39789 TATTTAAATATATA
1 TATATAAATATATA
*
39803 TATATATATATATA
1 TATATAAATATATA
39817 TA
1 TA
39819 AATATAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATATATA
Found at i:40189 original size:18 final size:19
Alignment explanation
Indices: 40156--40192 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40146 TAAAATAAAT
*
40156 TAGATAAATTAATTGATCA
1 TAGATAAATAAATTGATCA
40175 TAGATAAA-AAATTGATCA
1 TAGATAAATAAATTGATCA
40193 AATTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (19 bp):
TAGATAAATAAATTGATCA
Found at i:41314 original size:21 final size:21
Alignment explanation
Indices: 41274--41315 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41264 TTCCGTTTGT
*
41274 AACTGCAATTAACATGTCTGC
1 AACTGCAATTAACATCTCTGC
41295 AACTGCAATTTAA-ATCTCTGC
1 AACTGCAA-TTAACATCTCTGC
41316 TATAGCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (21 bp):
AACTGCAATTAACATCTCTGC
Found at i:45281 original size:24 final size:24
Alignment explanation
Indices: 45254--45303 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
45244 GTTGCAACTC
*
45254 AAGGAATG-CCCCTCAATAAGTAAA
1 AAGGAATGTCCAC-CAATAAGTAAA
45278 AAGGAATGTCCACCAATAAGTAAA
1 AAGGAATGTCCACCAATAAGTAAA
45302 AA
1 AA
45304 TTAAGTAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (24 bp):
AAGGAATGTCCACCAATAAGTAAA
Found at i:51882 original size:2 final size:2
Alignment explanation
Indices: 51875--51909 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
51865 ATTTTATTCT
51875 TA TA 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 TA TA T
51910 TAGAATTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52790 original size:16 final size:16
Alignment explanation
Indices: 52771--52832 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
52761 TTAAGTAACT
52771 TTTAAATTTAAAATAA
1 TTTAAATTTAAAATAA
* * *
52787 TTTAAATTTTACATGA
1 TTTAAATTTAAAATAA
*
52803 TTCAAATTTAAAATAA
1 TTTAAATTTAAAATAA
*
52819 TTTAAAATTAAAAT
1 TTTAAATTTAAAAT
52833 TTTTCAATCA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAAATAA
Found at i:52796 original size:23 final size:22
Alignment explanation
Indices: 52752--52797 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
52742 AATGTAAAAA
* *
52752 AAATTTAAATTAAGTAACTTTT
1 AAATTTAAAATAAGTAAATTTT
*
52774 AAATTTAAAATAATTTAAATTTT
1 AAATTTAAAATAA-GTAAATTTT
52797 A
1 A
52798 CATGATTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATTTAAAATAAGTAAATTTT
Found at i:52839 original size:32 final size:32
Alignment explanation
Indices: 52770--52839 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
52760 ATTAAGTAAC
* * *
52770 TTTT-AAATTTAAAATAATTTAAATTTTACAT
1 TTTTCAAATTTAAAATAATTTAAAATTAAAAT
**
52801 GATTCAAATTTAAAATAATTTAAAATTAAAAT
1 TTTTCAAATTTAAAATAATTTAAAATTAAAAT
52833 TTTTCAA
1 TTTTCAA
52840 TCATTAACTT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (32 bp):
TTTTCAAATTTAAAATAATTTAAAATTAAAAT
Found at i:53567 original size:21 final size:23
Alignment explanation
Indices: 53524--53568 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
53514 ATTAAGTTAA
**
53524 TTTTATTTTTCTCTTTTTTTATT
1 TTTTATTTTTCTCTTTTAATATT
53547 TTTTA-TTTT-TCTTTTAATATT
1 TTTTATTTTTCTCTTTTAATATT
53568 T
1 T
53569 ATGATAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 4 0.20
23 5 0.25
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTATTTTTCTCTTTTAATATT
Found at i:58725 original size:19 final size:19
Alignment explanation
Indices: 58703--58742 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
58693 TCAATTATTT
58703 AAGATTAAAGTAATTACAC
1 AAGATTAAAGTAATTACAC
58722 AAGATTAAAGTAATTACAC
1 AAGATTAAAGTAATTACAC
58741 AA
1 AA
58743 TGAATGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (19 bp):
AAGATTAAAGTAATTACAC
Found at i:59887 original size:12 final size:12
Alignment explanation
Indices: 59872--59896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59862 GTTGTCAGCA
59872 TAGTTAAAAACT
1 TAGTTAAAAACT
59884 TAGTTAAAAACT
1 TAGTTAAAAACT
59896 T
1 T
59897 TATCAAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TAGTTAAAAACT
Found at i:62276 original size:20 final size:21
Alignment explanation
Indices: 62246--62284 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
62236 ATTTAAAAAT
*
62246 TCTTAAAATTTTAAAATTTGA
1 TCTTAAAATTTAAAAATTTGA
62267 TCTT-AAATTTAAAAATTT
1 TCTTAAAATTTAAAAATTT
62285 TTAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (21 bp):
TCTTAAAATTTAAAAATTTGA
Found at i:63397 original size:15 final size:14
Alignment explanation
Indices: 63377--63408 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
63367 TAGAACATGT
63377 AATTTAAATAAATCA
1 AATTTAAATAAAT-A
63392 AATTTAAATAAATA
1 AATTTAAATAAATA
63406 AAT
1 AAT
63409 AAATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTTAAATAAATA
Found at i:63460 original size:11 final size:10
Alignment explanation
Indices: 63411--63466 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
63401 AAATAAATAA
63411 ATATTTATTT
1 ATATTTATTT
*
63421 ATGTTTA-TT
1 ATATTTATTT
63430 -TATTTATTTT
1 ATATTTA-TTT
*
63440 AAATTTATTT
1 ATATTTATTT
63450 ATATTTAATTT
1 ATATTT-ATTT
63461 ATATTT
1 ATATTT
63467 TATTAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 5 0.13
9 2 0.05
10 16 0.42
11 15 0.39
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
ATATTTATTT
Found at i:63472 original size:15 final size:15
Alignment explanation
Indices: 63413--63462 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
63403 ATAAATAAAT
*
63413 ATTTATTTATGTTT-
1 ATTTATTTATATTTA
63427 ATTTATTTAT-TTTAA
1 ATTTATTTATATTT-A
63442 ATTTATTTATATTTA
1 ATTTATTTATATTTA
63457 ATTTAT
1 ATTTAT
63463 ATTTTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.09
14 10 0.30
15 17 0.52
16 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
ATTTATTTATATTTA
Found at i:64606 original size:2 final size:2
Alignment explanation
Indices: 64599--64630 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
64589 AACATGTGTT
64599 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
64631 ATTTTGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64851 original size:20 final size:21
Alignment explanation
Indices: 64828--64870 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
64818 ATTATAAATA
64828 TTAAAAT-A-AAAATAATATTT
1 TTAAAATAATAAAATAA-ATTT
64848 TT-AAATAATAAAATAAATTT
1 TTAAAATAATAAAATAAATTT
64868 TTA
1 TTA
64871 TATCATTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATAATAAAATAAATTT
Found at i:65473 original size:21 final size:21
Alignment explanation
Indices: 65386--65475 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 21
65376 AATATATTTT
* *
65386 GATGAATGAATGCATTTGTTG
1 GATGAATGAATGTATTTATTG
* * *
65407 AATAAAT-AGATGTATTTGTTG
1 GATGAATGA-ATGTATTTATTG
* *
65428 GATGAATGAATGTATTTCTTA
1 GATGAATGAATGTATTTATTG
*
65449 GATGAGA-GAATGTACTTATTG
1 GATGA-ATGAATGTATTTATTG
65470 GATGAA
1 GATGAA
65476 AAAAATGTAC
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
20 2 0.04
21 52 0.93
22 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (21 bp):
GATGAATGAATGTATTTATTG
Found at i:65534 original size:16 final size:16
Alignment explanation
Indices: 65513--65543 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
65503 ATCATAGTTC
65513 GTGAAAAAACTTATTT
1 GTGAAAAAACTTATTT
65529 GTGAAAAAACTTATT
1 GTGAAAAAACTTATT
65544 AATTAAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (16 bp):
GTGAAAAAACTTATTT
Found at i:66595 original size:13 final size:13
Alignment explanation
Indices: 66577--66603 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
66567 AAATTATGCT
66577 TTGTATCGATACA
1 TTGTATCGATACA
66590 TTGTATCGATACA
1 TTGTATCGATACA
66603 T
1 T
66604 GATCATTGTA
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:66633 original size:20 final size:20
Alignment explanation
Indices: 66589--66662 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
66579 GTATCGATAC
66589 ATTGTATCGATACATGATC-
1 ATTGTATCGATACATGATCA
66608 ATTGTATCGATACATGGA-CA
1 ATTGTATCGATACAT-GATCA
* *
66628 ATTGTATCGATACATTATGA
1 ATTGTATCGATACATGATCA
66648 ATTGTATCGATACAT
1 ATTGTATCGATACAT
66663 TGCTTCTAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 17 0.34
20 33 0.66
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGATCA
Found at i:71845 original size:13 final size:13
Alignment explanation
Indices: 71827--71866 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
71817 ACAATATTTC
71827 TTGTATCGATACA
1 TTGTATCGATACA
71840 TTGTATCGATACA
1 TTGTATCGATACA
*
71853 TTATATCGATACA
1 TTGTATCGATACA
71866 T
1 T
71867 GGGTTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Done.