Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1806
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: 37698
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:889 original size:20 final size:20
Alignment explanation
Indices: 864--920 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
854 TTTTTACAAT
864 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
884 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
904 TTGTATCGATATATTGT
1 TTGTATCGATACATTGT
921 ATCGATACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:972 original size:20 final size:20
Alignment explanation
Indices: 947--1001 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
937 TTTACCCAGA
*
947 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
967 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
*
987 TGTATAGATACATTG
1 TGTATCGATACATTG
1002 TATCGATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:1000 original size:13 final size:13
Alignment explanation
Indices: 984--1013 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
974 ATACATTGCT
984 CATTGTATAGATA
1 CATTGTATAGATA
*
997 CATTGTATCGATA
1 CATTGTATAGATA
1010 CATT
1 CATT
1014 TTACGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATAGATA
Found at i:3390 original size:51 final size:50
Alignment explanation
Indices: 3325--3548 Score: 234
Period size: 51 Copynumber: 4.4 Consensus size: 50
3315 ATTTTTCATC
*
3325 TCGGGGATACTCCAATCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAA-CCCGATTTCATTTCCAAAACATCAATTTTTCTTAA
* * * * ** **
3376 TCGGGGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCGCAA
1 TCGGGGATACTCCAAC-CCGATTTCATTTCCAAAACATCAATTTTTCTTAA
* *
3427 CCGGGGATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAA-CCCGATTTCATTTCCAAAACATCAATTTTTCTTAA
* * *
3478 TCGGGGATACTCCAACTCCGATTTTATTTTCAAAA-AGTACAAATTTTTCATAA
1 TCGGGGATACTCCAAC-CCGATTTCATTTCCAAAACA-T-C-AATTTTTCTTAA
* *
3531 TTGGGGAAACTCCAACCC
1 TCGGGGATACTCCAACCC
3549 CGTCATTTCA
Statistics
Matches: 141, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
50 3 0.02
51 109 0.77
52 4 0.03
53 25 0.18
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (50 bp):
TCGGGGATACTCCAACCCGATTTCATTTCCAAAACATCAATTTTTCTTAA
Found at i:3572 original size:28 final size:28
Alignment explanation
Indices: 3534--3604 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
3524 TTCATAATTG
*
3534 GGGAA-ACTCCAACCCCGTCATTT-CATC
1 GGGAATACTCCAACCCCGTCATTTCCA-A
*
3561 GGGAATACTCCAACCCCGTTATTTCCAA
1 GGGAATACTCCAACCCCGTCATTTCCAA
*
3589 GGGGATACTCCAACCC
1 GGGAATACTCCAACCC
3605 TAGCTTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 5 0.13
28 32 0.82
29 2 0.05
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (28 bp):
GGGAATACTCCAACCCCGTCATTTCCAA
Found at i:3621 original size:109 final size:108
Alignment explanation
Indices: 3480--3732 Score: 240
Period size: 109 Copynumber: 2.3 Consensus size: 108
3470 TTTCTTAATC
* * * * * *
3480 GGGGATACTCCAACTCCGATTTTATTTTCAAAA-AGTACAAATTTTTCATAATTGGGGAAACTCC
1 GGGGATACTCCAAC-CCGACTTTATATCCAAAATAGTA-AAAGTTTTCATAATCGGGGAAACTAC
* *
3544 AACCCCGTCATTTCATC-GGGAATACTCCAACCCCGTTATTTCCAA
64 AACCCCATCATGTCATCAGGG-ATACTCCAACCCCGTTATTTCCAA
* * * ** *
3589 GGGGATACTCCAACCCTAGCTTTATATCCAAAATATTAATAGTTTTCATAATCGGGGGTACTATA
1 GGGGATACTCCAACCCGA-CTTTATATCCAAAATAGTAAAAGTTTTCATAATCGGGGAAACTACA
* * * * * *
3654 ACCCCATTATGTCATCAGGGATACTCTAATCCTGTTATTTTCGA
65 ACCCCATCATGTCATCAGGGATACTCCAACCCCGTTATTTCCAA
* * *
3698 GGGGATACTCCAACCCCGATTTTATTTCTAAAATA
1 GGGGATACTCCAA-CCCGACTTTATATCCAAAATA
3733 CCAATTTTTC
Statistics
Matches: 116, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
108 3 0.03
109 103 0.89
110 10 0.09
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (108 bp):
GGGGATACTCCAACCCGACTTTATATCCAAAATAGTAAAAGTTTTCATAATCGGGGAAACTACAA
CCCCATCATGTCATCAGGGATACTCCAACCCCGTTATTTCCAA
Found at i:3761 original size:51 final size:51
Alignment explanation
Indices: 3701--3815 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
3691 TTTTCGAGGG
* *
3701 GATACTCCAACCCCGATTTTA-TTTCTAAAATACCAATTTTTCACAATC-ACA
1 GATACTCCAACCCCGATTTTAGTTTC-AAAACACCAATTTCTCACAATCGA-A
* *
3752 GATACTCCAACTCCGATTTTAGTTTCAAAACCCCAATTTCTCACAATCGAA
1 GATACTCCAACCCCGATTTTAGTTTCAAAACACCAATTTCTCACAATCGAA
3803 GATACTCCAACCC
1 GATACTCCAACCC
3816 TGTTATTTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 52 0.91
52 5 0.09
ACGTcount: A:0.34, C:0.30, G:0.06, T:0.30
Consensus pattern (51 bp):
GATACTCCAACCCCGATTTTAGTTTCAAAACACCAATTTCTCACAATCGAA
Found at i:3895 original size:52 final size:51
Alignment explanation
Indices: 3828--3942 Score: 135
Period size: 52 Copynumber: 2.2 Consensus size: 51
3818 TTATTTTCAT
*
3828 GGGGATACTCCAACCCCGGC-CTTATTTCTA-AAGCATCGATTTTTTCACAATC
1 GGGGATACTCCAACCCC-GCTCTTATTTCTAGAA-CACCGA-TTTTTCACAATC
* * * * *
3880 GGGGATACTCTAACCCCGCTTTTTTTTTTAGAACACCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGCTCTTATTTCTAGAACACCGATTTTTCACAATC
3931 GGGGATACTCCA
1 GGGGATACTCCA
3943 GCCCTGTTGT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
51 24 0.44
52 28 0.52
53 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGCTCTTATTTCTAGAACACCGATTTTTCACAATC
Found at i:5215 original size:52 final size:51
Alignment explanation
Indices: 5159--5311 Score: 157
Period size: 51 Copynumber: 2.9 Consensus size: 51
5149 ACTGCCAAAG
* * *
5159 AAATGTATCGATACATTAATAAATGTATCGATGCATCTA-GATTTGTTTTA-CC
1 AAATGTATCGATACATTAATCAATGTATCGATACATCTAGGA---ATTTTACCC
** * *
5211 AAATGTATCGATATGTTTATCATTGTATCGATACATCTAGGAATTTTACCC
1 AAATGTATCGATACATTAATCAATGTATCGATACATCTAGGAATTTTACCC
* * *
5262 AGATGTATCGATACATTATTCAATGTATCGATACATGTAGGTAAATTTTA
1 AAATGTATCGATACATTAATCAATGTATCGATACATCTAGG--AATTTTA
5312 ATATTTCGTG
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
50 5 0.06
51 36 0.43
52 33 0.40
53 9 0.11
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (51 bp):
AAATGTATCGATACATTAATCAATGTATCGATACATCTAGGAATTTTACCC
Found at i:8146 original size:13 final size:13
Alignment explanation
Indices: 8128--8185 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
8118 GGGCTTTCAC
8128 ATGTATCGATACA
1 ATGTATCGATACA
8141 ATGTATCGATAC-
1 ATGTATCGATACA
*
8153 AT-T-TC---ACC
1 ATGTATCGATACA
*
8161 ATGTATTGATACA
1 ATGTATCGATACA
8174 ATGTATCGATAC
1 ATGTATCGATAC
8186 TGAGTGAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
9 1 0.03
10 3 0.08
11 1 0.03
12 2 0.06
13 25 0.69
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:8165 original size:33 final size:32
Alignment explanation
Indices: 8122--8185 Score: 110
Period size: 33 Copynumber: 2.0 Consensus size: 32
8112 GCCGTTGGGC
8122 TTTCACATGTATCGATACAATGTATCGATACA
1 TTTCACATGTATCGATACAATGTATCGATACA
*
8154 TTTCACCATGTATTGATACAATGTATCGATAC
1 TTTCA-CATGTATCGATACAATGTATCGATAC
8186 TGAGTGAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 5 0.17
33 25 0.83
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (32 bp):
TTTCACATGTATCGATACAATGTATCGATACA
Found at i:10463 original size:17 final size:16
Alignment explanation
Indices: 10438--10471 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
10428 CAAAAAACTT
10438 ATAATAAAATAAAATA
1 ATAATAAAATAAAATA
*
10454 ATAATCAAAATACAATA
1 ATAAT-AAAATAAAATA
10471 A
1 A
10472 CTAGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (16 bp):
ATAATAAAATAAAATA
Found at i:11058 original size:25 final size:25
Alignment explanation
Indices: 11012--11060 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
11002 ATTATTTATT
*
11012 TAAAAGATAAATATCTATGTAAATC
1 TAAAAGATAAATATCTACGTAAATC
11037 TAAAAGATAAATA-CATACGTAAAT
1 TAAAAGATAAATATC-TACGTAAAT
11061 AATTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (25 bp):
TAAAAGATAAATATCTACGTAAATC
Found at i:11925 original size:20 final size:20
Alignment explanation
Indices: 11888--11926 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11878 ATTTATAAGG
* *
11888 ACTTTTTCTGATGGAATTTC
1 ACTTTTTCTAATGAAATTTC
*
11908 ACTTTTTTTAATGAAATTT
1 ACTTTTTCTAATGAAATTT
11927 TTGGTAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (20 bp):
ACTTTTTCTAATGAAATTTC
Found at i:12664 original size:14 final size:14
Alignment explanation
Indices: 12645--12672 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12635 AAGTATTTTC
12645 AAATAAATTCAAAA
1 AAATAAATTCAAAA
12659 AAATAAATTCAAAA
1 AAATAAATTCAAAA
12673 TATTTAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATTCAAAA
Found at i:16237 original size:21 final size:22
Alignment explanation
Indices: 16183--16237 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
16173 TAGAACAAAT
*
16183 ATTAGAGAGAGAAGAACAGAGA
1 ATTAGAGAAAGAAGAACAGAGA
* * *
16205 ATTAAAGGAAGAA-AATAGAGA
1 ATTAGAGAAAGAAGAACAGAGA
16226 ATTAGAGAAAGA
1 ATTAGAGAAAGA
16238 TTAGAATTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.58, C:0.02, G:0.27, T:0.13
Consensus pattern (22 bp):
ATTAGAGAAAGAAGAACAGAGA
Found at i:17920 original size:2 final size:2
Alignment explanation
Indices: 17913--17943 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17903 TTAAATATTT
17913 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
17944 GCAAATTAAG
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:19258 original size:23 final size:22
Alignment explanation
Indices: 19224--19272 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
19214 AATAATTTTT
*
19224 TTAATATTTTTATAAAAATTAA
1 TTAATATATTTATAAAAATTAA
*
19246 TTAATCATATTTATAAACATTAA
1 TTAAT-ATATTTATAAAAATTAA
19269 TTAA
1 TTAA
19273 AAATTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAATATATTTATAAAAATTAA
Found at i:22195 original size:21 final size:20
Alignment explanation
Indices: 22165--22203 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22155 CTTTTCTATG
*
22165 AAAATAAATATATTGTTTTTA
1 AAAATAAATAAATT-TTTTTA
*
22186 AAAATGAATAAATTTTTT
1 AAAATAAATAAATTTTTT
22204 ATATTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
AAAATAAATAAATTTTTTTA
Found at i:22934 original size:27 final size:28
Alignment explanation
Indices: 22904--22959 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
22894 TATATATTAT
* *
22904 ATTTTAATAAAT-TTTTAATTAAATTTA
1 ATTTGAATAAATAATTTAATTAAATTTA
* *
22931 ATTTGATTAAATAATTTATTTAAATTTA
1 ATTTGAATAAATAATTTAATTAAATTTA
22959 A
1 A
22960 CTTAATTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTGAATAAATAATTTAATTAAATTTA
Found at i:30857 original size:19 final size:19
Alignment explanation
Indices: 30812--30889 Score: 67
Period size: 18 Copynumber: 4.3 Consensus size: 19
30802 AAAATAAAAC
* *
30812 ATAAATAAT-AATTAATAT
1 ATAAATATTAAATTATTAT
30830 -TAAAT-TTAAATTATTAT
1 ATAAATATTAAATTATTAT
*
30847 ATAAATATTAAATAATT-T
1 ATAAATATTAAATTATTAT
*
30865 ATAAA-ATATAAAATATTAT
1 ATAAATAT-TAAATTATTAT
*
30884 TTAAAT
1 ATAAAT
30890 TAATTTTCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.02
17 15 0.31
18 18 0.38
19 14 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAATATTAAATTATTAT
Found at i:31291 original size:21 final size:21
Alignment explanation
Indices: 31267--31314 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
31257 AATAATTGAA
31267 ATTTATAA-AAATAAAATATTT
1 ATTTATAATAAATAAAA-ATTT
*
31288 ATTT-TAATTAATTAAAAATTT
1 ATTTATAA-TAAATAAAAATTT
31309 ATTTAT
1 ATTTAT
31315 CTTTTTGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 12 0.52
22 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTATAATAAATAAAAATTT
Found at i:31398 original size:17 final size:19
Alignment explanation
Indices: 31364--31398 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
31354 TAATTTGGTA
31364 AAATATTAAATAATTTATC
1 AAATATTAAATAATTTATC
31383 AAATA-TAAAT-ATTTAT
1 AAATATTAAATAATTTAT
31399 TTACATTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTAAATAATTTATC
Found at i:32245 original size:18 final size:19
Alignment explanation
Indices: 32216--32255 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
32206 AATAAATATT
32216 TTATATTTTTATAAATTAA
1 TTATATTTTTATAAATTAA
32235 TTATA-TTTTATAAATTAA
1 TTATATTTTTATAAATTAA
32253 TTA
1 TTA
32256 AAATTGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATATTTTTATAAATTAA
Found at i:33118 original size:18 final size:19
Alignment explanation
Indices: 33089--33124 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
33079 AATTTAAAAA
*
33089 TTTTATATAAAAATAATTC
1 TTTTATATAAAAACAATTC
33108 TTTTA-ATAAAAACAATT
1 TTTTATATAAAAACAATT
33125 TGATAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTTATATAAAAACAATTC
Found at i:34284 original size:52 final size:51
Alignment explanation
Indices: 34177--34290 Score: 133
Period size: 51 Copynumber: 2.2 Consensus size: 51
34167 ACACCTTATT
** **
34177 TGCAAATAAGGGGTGCCTTAATTAATAAGGCATGTCTTATTTCGTTAAAGG
1 TGCAAATAAGGGGTGCCTTAATTAATAAGGCATGAATTATTTCAATAAAGG
*
34228 TGCAAATAAGGTGTGCCTTAATTAAATAAGG-ATGAATTATTTGCAA-ATAAGG
1 TGCAAATAAGGGGTGCCTTAATT-AATAAGGCATGAATTATTT-CAATA-AAGG
*
34280 TGCAAACAAGG
1 TGCAAATAAGG
34291 CATGCGTAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
51 32 0.59
52 22 0.41
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (51 bp):
TGCAAATAAGGGGTGCCTTAATTAATAAGGCATGAATTATTTCAATAAAGG
Found at i:34696 original size:19 final size:19
Alignment explanation
Indices: 34672--34710 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
34662 AAATTACATA
34672 TAATTACATAAAATATTAC
1 TAATTACATAAAATATTAC
*
34691 TAATTATATAAAATATTAC
1 TAATTACATAAAATATTAC
34710 T
1 T
34711 TTGACATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTACATAAAATATTAC
Found at i:34743 original size:22 final size:23
Alignment explanation
Indices: 34718--34761 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
34708 ACTTTGACAT
34718 CTAATTATAA-TTACATAAAACA
1 CTAATTATAAGTTACATAAAACA
34740 CTAATTATAAGTTACATAAAAC
1 CTAATTATAAGTTACATAAAAC
34762 GTTACTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (23 bp):
CTAATTATAAGTTACATAAAACA
Found at i:34767 original size:57 final size:53
Alignment explanation
Indices: 34670--34813 Score: 122
Period size: 57 Copynumber: 2.7 Consensus size: 53
34660 CAAAATTACA
* *
34670 TATAATTACATAAAATATTACTAATTATATAAAATATTACTTTGACATCTAAT
1 TATAATTACATAAAATATTACTAATTACATAAAACATTACTTTGACATCTAAT
* *
34723 TATAATTACATAAAACACTAATTA-TAAGTTACATAAAACGTTACTTT--TA-C--AT
1 TATAATTACAT-AAA-A-T-ATTACTAA-TTACATAAAACATTACTTTGACATCTAAT
* * *
34775 T-TGATTACATAAAATATTATTAATTACGTATAAACATTA
1 TATAATTACATAAAATATTACTAATTACATA-AAACATTA
34814 ATAATTATAT
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
47 10 0.13
48 11 0.14
49 1 0.01
50 3 0.04
51 8 0.10
52 3 0.04
53 11 0.14
54 4 0.05
55 2 0.03
56 4 0.05
57 20 0.26
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (53 bp):
TATAATTACATAAAATATTACTAATTACATAAAACATTACTTTGACATCTAAT
Found at i:34830 original size:19 final size:19
Alignment explanation
Indices: 34778--34851 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
34768 TTTACATTTG
* * *
34778 ATTACATAAAATATTATTA
1 ATTATATAAAACATTAATA
34797 ATTACGTAT-AAACATTAATA
1 ATTA--TATAAAACATTAATA
34817 ATTATATAAAACATTAGAT-
1 ATTATATAAAACATTA-ATA
* *
34836 ATTAAATAAAATATTA
1 ATTATATAAAACATTA
34852 TATTCGCATG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.07
19 26 0.57
20 15 0.33
21 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
ATTATATAAAACATTAATA
Found at i:34897 original size:20 final size:19
Alignment explanation
Indices: 34862--34912 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
34852 TATTCGCATG
34862 TAATTACATAAAATATTAC
1 TAATTACATAAAATATTAC
*
34881 TAATTATATATAAATATTAC
1 TAATTACATA-AAATATTAC
34901 -AAGTTACATAAA
1 TAA-TTACATAAA
34913 CGTTACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (19 bp):
TAATTACATAAAATATTAC
Found at i:34933 original size:66 final size:67
Alignment explanation
Indices: 34862--35015 Score: 190
Period size: 66 Copynumber: 2.3 Consensus size: 67
34852 TATTCGCATG
* * * * *
34862 TAATTACATAAAATATTACTAATTATATATAAATATTACAAGTTACAT-AAACGTTACTTTTATA
1 TAATTACATAAAATATTACTAATTACATATAAATATTACAAGTTACATAAAACATTACCTTAACA
34926 TGA
66 T-A
* *
34929 -AATTA-AAACAAATATTA-TCAATTACATATAAATGTTACAAGTTACATAAAACATTACCTTAA
1 TAATTACATA-AAATATTACT-AATTACATATAAATATTACAAGTTACATAAAACATTACCTTAA
34991 CATA
64 CATA
34995 TAATTACATAAAATATTACTA
1 TAATTACATAAAATATTACTA
35016 GTTTTCATCA
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
65 3 0.04
66 40 0.55
67 27 0.37
68 3 0.04
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.36
Consensus pattern (67 bp):
TAATTACATAAAATATTACTAATTACATATAAATATTACAAGTTACATAAAACATTACCTTAACA
TA
Found at i:36382 original size:22 final size:22
Alignment explanation
Indices: 36342--36388 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
36332 TAAGATACAA
* **
36342 TTTTTTTTTTCAATTTTTTTAG
1 TTTTTCTTTTCAAGCTTTTTAG
*
36364 TTTTTCTTTTCAAGCTTTTTCG
1 TTTTTCTTTTCAAGCTTTTTAG
36386 TTT
1 TTT
36389 CTCTCTCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (22 bp):
TTTTTCTTTTCAAGCTTTTTAG
Done.