Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3004
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: 64706
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Found at i:3160 original size:21 final size:22
Alignment explanation
Indices: 3135--3181 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
3125 GTTTCGTTTC
*
3135 AATTTTGTTTG-TTTGTTTAAT
1 AATTTTATTTGTTTTGTTTAAT
3156 AA-TTTATTTGTTTTGTTTAAT
1 AATTTTATTTGTTTTGTTTAAT
3177 AATTT
1 AATTT
3182 ACTTAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 14 0.61
22 2 0.09
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (22 bp):
AATTTTATTTGTTTTGTTTAAT
Found at i:3182 original size:21 final size:20
Alignment explanation
Indices: 3142--3182 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
3132 TTCAATTTTG
3142 TTTGTTTGTTTAATAATTTA
1 TTTGTTTGTTTAATAATTTA
3162 TTTGTTTTGTTTAATAATTTA
1 TTTG-TTTGTTTAATAATTTA
3183 CTTAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTGTTTGTTTAATAATTTA
Found at i:4545 original size:23 final size:23
Alignment explanation
Indices: 4513--4557 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
4503 GCCTGCACAC
*
4513 TTAACCCATTCCCATGCTACCCA
1 TTAACACATTCCCATGCTACCCA
4536 TTAACACATTCCCATGCTACCC
1 TTAACACATTCCCATGCTACCC
4558 GCAGCCCTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.42, G:0.04, T:0.27
Consensus pattern (23 bp):
TTAACACATTCCCATGCTACCCA
Found at i:12524 original size:24 final size:24
Alignment explanation
Indices: 12488--12559 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
12478 TTGAAACCAG
*
12488 TTCCCCAGCTCCTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
* *
12512 TTCCACTGTTCCTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
*
12536 TTCCACAGCTCTTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
12560 ATCGATTGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.10, C:0.49, G:0.04, T:0.38
Consensus pattern (24 bp):
TTCCACAGCTCCTCTCTTCACCCT
Found at i:15025 original size:34 final size:34
Alignment explanation
Indices: 14967--15032 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
14957 GAAACACTAG
*
14967 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGAAAATCATTTTAC-GAAAAGT
*
15002 AAAATATTTTTCA-AAAATCATTTTACGAAAA
1 AAAATATTTTCCAGAAAATCATTTTACGAAAA
15033 ATATTTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (34 bp):
AAAATATTTTCCAGAAAATCATTTTACGAAAAGT
Found at i:15032 original size:14 final size:13
Alignment explanation
Indices: 15002--15040 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
14992 ACAGAAAAGT
*
15002 AAAATATTTTTCA
1 AAAATATTTTACA
15015 AAAATCATTTTACGA
1 AAAAT-ATTTTAC-A
15030 AAAATATTTTA
1 AAAATATTTTA
15041 GTGCCTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
15 6 0.26
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (13 bp):
AAAATATTTTACA
Found at i:16410 original size:78 final size:78
Alignment explanation
Indices: 16310--16460 Score: 230
Period size: 78 Copynumber: 1.9 Consensus size: 78
16300 CTCATTTTCC
* *
16310 ACCATTAAACCATGATCCCTTGATCTCACCAACTGGGAGAGTCGGTGATCATGTTAATAATGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
16375 ACCATGGAGTTCG
66 ACCATGGAGTTCG
* * * * *
16388 ACCATTAAACCATGATCCCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
*
16453 ATCATGGA
66 ACCATGGA
16461 CTTTGTGTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (78 bp):
ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
ACCATGGAGTTCG
Found at i:19022 original size:9 final size:9
Alignment explanation
Indices: 19008--19075 Score: 91
Period size: 9 Copynumber: 7.6 Consensus size: 9
18998 TTTGGTTAAA
19008 AATTACCCG
1 AATTACCCG
19017 AATTACCCG
1 AATTACCCG
*
19026 AATTATCCG
1 AATTACCCG
*
19035 AATTATCCG
1 AATTACCCG
**
19044 AATTAATCG
1 AATTACCCG
19053 AATTACCCG
1 AATTACCCG
*
19062 AATTACCTG
1 AATTACCCG
19071 AATTA
1 AATTA
19076 ATCGAATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTACCCG
Found at i:19046 original size:27 final size:27
Alignment explanation
Indices: 19009--19084 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
18999 TTGGTTAAAA
** *
19009 ATTACCCGAATTACCCGAATTATCCGA
1 ATTACCCGAATTAATCGAATTACCCGA
*
19036 ATTATCCGAATTAATCGAATTACCCGA
1 ATTACCCGAATTAATCGAATTACCCGA
*
19063 ATTACCTGAATTAATCGAATTA
1 ATTACCCGAATTAATCGAATTA
19085 ACCTAATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (27 bp):
ATTACCCGAATTAATCGAATTACCCGA
Found at i:19092 original size:18 final size:18
Alignment explanation
Indices: 19008--19097 Score: 67
Period size: 18 Copynumber: 4.9 Consensus size: 18
18998 TTTGGTTAAA
* **
19008 AATTACCCGAATTACCCG
1 AATTAACCGAATTAATCG
*
19026 AATTATCCGAATT-ATCCG
1 AATTAACCGAATTAAT-CG
* **
19044 AATTAATCGAATTACCCG
1 AATTAACCGAATTAATCG
19062 AATT-ACCTGAATTAATCG
1 AATTAACC-GAATTAATCG
*
19080 AATTAACCTAATTGAATC
1 AATTAACCGAATT-AATC
19098 ATACATAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
17 2 0.04
18 47 0.84
19 7 0.12
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (18 bp):
AATTAACCGAATTAATCG
Found at i:19092 original size:27 final size:26
Alignment explanation
Indices: 19008--19092 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 26
18998 TTTGGTTAAA
** *
19008 AATTACCCGAATTACCCGAATTATCCG
1 AATTA-CCGAATTAATCGAATTAACCG
*
19035 AATTATCCGAATTAATCGAATTACCCG
1 AATTA-CCGAATTAATCGAATTAACCG
*
19062 AATTACCTGAATTAATCGAATTAACCT
1 AATTACC-GAATTAATCGAATTAACCG
19089 AATT
1 AATT
19093 GAATCATACA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
26 2 0.04
27 49 0.96
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (26 bp):
AATTACCGAATTAATCGAATTAACCG
Found at i:19182 original size:18 final size:19
Alignment explanation
Indices: 19159--19197 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
19149 TTATAGAATT
* *
19159 TTATTTTTATTTTTTA-AA
1 TTATTTGTAATTTTTATAA
19177 TTATTTGTAATTTTTATAA
1 TTATTTGTAATTTTTATAA
19196 TT
1 TT
19198 GGGATGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTATTTGTAATTTTTATAA
Found at i:19564 original size:20 final size:20
Alignment explanation
Indices: 19539--19580 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
19529 CATAGCAAAA
19539 GGACATTAGTGAAATGTTGT
1 GGACATTAGTGAAATGTTGT
*
19559 GGACATTAGTGCAATGTTGT
1 GGACATTAGTGAAATGTTGT
19579 GG
1 GG
19581 TCAGCTACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (20 bp):
GGACATTAGTGAAATGTTGT
Found at i:29166 original size:25 final size:26
Alignment explanation
Indices: 29134--29188 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
29124 TTATTAAATT
*
29134 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
29159 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
29184 A-ATAT
1 ATATAT
29189 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:29375 original size:44 final size:45
Alignment explanation
Indices: 29326--29420 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
29316 TTACACCTCT
* *
29326 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
29370 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
29415 ATTACA
1 ATTACA
29421 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:29420 original size:16 final size:16
Alignment explanation
Indices: 29401--29452 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
29391 GATTTGCTAT
* *
29401 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
29417 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29433 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29449 TACA
1 TACA
29453 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:33176 original size:19 final size:20
Alignment explanation
Indices: 33152--33190 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
33142 CAATTGTTTT
33152 AAAA-TTAA-ATAAGTTTAAA
1 AAAATTTAATATAA-TTTAAA
33171 AAAATTTAATATAATTTAAA
1 AAAATTTAATATAATTTAAA
33191 TTTTTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAATTTAATATAATTTAAA
Found at i:34790 original size:218 final size:218
Alignment explanation
Indices: 34412--35067 Score: 1285
Period size: 218 Copynumber: 3.0 Consensus size: 218
34402 TTCTTAATAG
34412 AACTTTGGATATGTGGTAAATATTTTCGTTTTAGGGAGTAAATTCTGGTACAGAAATTCCATAGT
1 AACTTTGGATATGTGGTAAATATTTTCGTTTTAGGGAGTAAATTCTGGTACAGAAATTCCATAGT
34477 AGTCTAACATCATCTATGTATTCAATTGAATGTGTTTTCCGTCTTTTAAGGATTCAGAAAGTGAT
66 AGTCTAACATCATCTATGTATTCAATTGAATGTGTTTTCCGTCTTTTAAGGATTCAGAAAGTGAT
34542 TTGTTTGTAATTTATGCTTTTGGTTGGTTTAAAATAGTTTAACTATTTTAATGTGACAGTCCAGA
131 TTGTTTGTAATTTATGCTTTTGGTTGGTTTAAAATAGTTTAACTATTTTAATGTGACAGTCCAGA
34607 TAGCCTAATGGTCTCGTGTATAA
196 TAGCCTAATGGTCTCGTGTATAA
34630 AACTTTGGATATGTGGTAAATATTTTCGTTTTAGGGAGTAAATTCTGGTACAGAAATTCCATAGT
1 AACTTTGGATATGTGGTAAATATTTTCGTTTTAGGGAGTAAATTCTGGTACAGAAATTCCATAGT
* *
34695 AGTCTAGCATCATCTATGTATTCAATTGAATGTGTTTTCCGTCTTTTAAGTATTCAGAAAGTGAT
66 AGTCTAACATCATCTATGTATTCAATTGAATGTGTTTTCCGTCTTTTAAGGATTCAGAAAGTGAT
34760 TTGTTTGTAATTTATGCTTTTGGTTGGTTTAAAATAGTTTAACTATTTTAATGTGACAGTCCAGA
131 TTGTTTGTAATTTATGCTTTTGGTTGGTTTAAAATAGTTTAACTATTTTAATGTGACAGTCCAGA
34825 TAGCCTAATGGTCTCGTGTATAA
196 TAGCCTAATGGTCTCGTGTATAA
34848 AACTTTGGATATGTGGTAAATATTTTCGTTTTAGGGAGTAAATTCTGGTACAGAAATTCCATAGT
1 AACTTTGGATATGTGGTAAATATTTTCGTTTTAGGGAGTAAATTCTGGTACAGAAATTCCATAGT
*
34913 AGTCTAACATCATCTATGTATTCAATTGAATGTGTTTTCCGTCTTTTAAGGATTCAAAAAGTGAT
66 AGTCTAACATCATCTATGTATTCAATTGAATGTGTTTTCCGTCTTTTAAGGATTCAGAAAGTGAT
34978 TTGTTTGTAATTTATGCTTTTGGTTGGTTTAAAATAGTTTAACTATTTTAATGTGACAGTCCAGA
131 TTGTTTGTAATTTATGCTTTTGGTTGGTTTAAAATAGTTTAACTATTTTAATGTGACAGTCCAGA
35043 TAGCCTAATGGTCTCGTGTATAA
196 TAGCCTAATGGTCTCGTGTATAA
35066 AA
1 AA
35068 ATCTGCTTTC
Statistics
Matches: 433, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
218 433 1.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (218 bp):
AACTTTGGATATGTGGTAAATATTTTCGTTTTAGGGAGTAAATTCTGGTACAGAAATTCCATAGT
AGTCTAACATCATCTATGTATTCAATTGAATGTGTTTTCCGTCTTTTAAGGATTCAGAAAGTGAT
TTGTTTGTAATTTATGCTTTTGGTTGGTTTAAAATAGTTTAACTATTTTAATGTGACAGTCCAGA
TAGCCTAATGGTCTCGTGTATAA
Found at i:35723 original size:36 final size:36
Alignment explanation
Indices: 35676--35748 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
35666 TGAACACTTG
35676 GCTGTTTTCATTTAATCTACAGTTAATATATATTTA
1 GCTGTTTTCATTTAATCTACAGTTAATATATATTTA
35712 GCTGTTTTCATTTAATCTACAGTTAATATATATTTA
1 GCTGTTTTCATTTAATCTACAGTTAATATATATTTA
35748 G
1 G
35749 GGCCACTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (36 bp):
GCTGTTTTCATTTAATCTACAGTTAATATATATTTA
Found at i:37282 original size:31 final size:31
Alignment explanation
Indices: 37212--37293 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
37202 AAATGGGCAG
37212 AATAAGCACTGAATTTATTTTACAACGTTTT
1 AATAAGCACTGAATTTATTTTACAACGTTTT
* *
37243 AATGAGCACTAAATTTATTTTACAACGTTTT
1 AATAAGCACTGAATTTATTTTACAACGTTTT
** *
37274 CGTAAGCACCGAATTTATTT
1 AATAAGCACTGAATTTATTT
37294 CATTCTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (31 bp):
AATAAGCACTGAATTTATTTTACAACGTTTT
Found at i:37486 original size:15 final size:15
Alignment explanation
Indices: 37466--37549 Score: 64
Period size: 15 Copynumber: 5.5 Consensus size: 15
37456 CTGATGTAGT
37466 TATCCTGGCTTGGGA
1 TATCCTGGCTTGGGA
** *
37481 TATCCTATTCTAGGGA
1 TATCCT-GGCTTGGGA
*
37497 TATCCCGGCTTGGGA
1 TATCCTGGCTTGGGA
* *
37512 TATCACAT-TC-TAGGA
1 TATC-C-TGGCTTGGGA
*
37527 TATCCCGGCTTGGGA
1 TATCCTGGCTTGGGA
37542 TATCCTGG
1 TATCCTGG
37550 GATATCCTAT
Statistics
Matches: 50, Mismatches: 14, Indels: 10
0.68 0.19 0.14
Matches are distributed among these distances:
14 2 0.04
15 35 0.70
16 13 0.26
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (15 bp):
TATCCTGGCTTGGGA
Found at i:37530 original size:30 final size:31
Alignment explanation
Indices: 37466--37547 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
37456 CTGATGTAGT
*
37466 TATCCTGGCTTGGGATATCCTATTCTAGGGA
1 TATCCCGGCTTGGGATATCCTATTCTAGGGA
37497 TATCCCGGCTTGGGATATCAC-ATTCTA-GGA
1 TATCCCGGCTTGGGATATC-CTATTCTAGGGA
37527 TATCCCGGCTTGGGATATCCT
1 TATCCCGGCTTGGGATATCCT
37548 GGGATATCCT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
29 1 0.02
30 22 0.46
31 24 0.50
32 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (31 bp):
TATCCCGGCTTGGGATATCCTATTCTAGGGA
Found at i:37562 original size:40 final size:41
Alignment explanation
Indices: 37507--37583 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
37497 TATCCCGGCT
37507 TGGGATATCACATTCTA-GGATATCCCGGCTTGGGATATCC
1 TGGGATATCACATTCTAGGGATATCCCGGCTTGGGATATCC
37547 TGGGATATC-CTATTCTAGGGATATCCCGGCTTGGGAT
1 TGGGATATCAC-ATTCTAGGGATATCCCGGCTTGGGAT
37584 CTAGGGGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
39 1 0.03
40 15 0.43
41 19 0.54
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (41 bp):
TGGGATATCACATTCTAGGGATATCCCGGCTTGGGATATCC
Found at i:38805 original size:44 final size:45
Alignment explanation
Indices: 38724--38811 Score: 103
Period size: 44 Copynumber: 2.0 Consensus size: 45
38714 CTGTTTATGG
*
38724 TCGTGATTTGTTTTTGTTATAATTGTGTTTTAAAGGTA-TCATGA
1 TCGTGATTTGTTTTTGTTATAATTGCGTTTTAAAGGTATTCATGA
*
38768 TCGTG-TTGTGTTTTTGTTTCATAATTGCG-TTT-GAGGTATTCATG
1 TCGTGATT-TGTTTTTG-TT-ATAATTGCGTTTTAAAGGTATTCATG
38812 TTAATAACTG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
43 2 0.05
44 18 0.47
45 10 0.26
46 8 0.21
ACGTcount: A:0.18, C:0.07, G:0.23, T:0.52
Consensus pattern (45 bp):
TCGTGATTTGTTTTTGTTATAATTGCGTTTTAAAGGTATTCATGA
Found at i:42968 original size:21 final size:21
Alignment explanation
Indices: 42944--42999 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
42934 TATGCTGTCT
42944 CGGTTCAATATTTTTGG-TGCC
1 CGGTTCAATATTTTTGGATG-C
** *
42965 CGGTTCAGCAGTTTTGGATGC
1 CGGTTCAATATTTTTGGATGC
42986 CGGTTC-ATATTTTT
1 CGGTTCAATATTTTT
43000 AACGTGTTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 5 0.18
21 21 0.75
22 2 0.07
ACGTcount: A:0.14, C:0.18, G:0.25, T:0.43
Consensus pattern (21 bp):
CGGTTCAATATTTTTGGATGC
Found at i:49093 original size:15 final size:15
Alignment explanation
Indices: 49073--49101 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49063 TATGTTCTTG
49073 ATCATTAAAATTTTA
1 ATCATTAAAATTTTA
49088 ATCATTAAAATTTT
1 ATCATTAAAATTTT
49102 CTCACCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCATTAAAATTTTA
Found at i:49485 original size:516 final size:518
Alignment explanation
Indices: 48563--49513 Score: 1640
Period size: 516 Copynumber: 1.8 Consensus size: 518
48553 TCGATTTCCT
* *
48563 TTTTAATTATTAAAATTTTCTCACCTTGTGCAGTTTCTCCCCATAATCCTCAGACTGTATCTTTC
1 TTTTAATCATTAAAATTTTCTCACCTTGTGCAGGTTCTCCCCATAATCCTCAGACTGTATCTTTC
* * *
48628 TTGGAATTGCTAGATCTTCCTTATGTTCTTGATAATGCATTGGACTCCAGGGATACTCCTGTTTC
66 TTGGAATTGCTAGA--TTCCTTATGTTCTTGACAATGCATCGGACTCCAGGGATACTCCTGCTTC
*
48693 ATTGCCTCAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATATTACAG
129 ATTGCCTAAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATATTACAG
* *
48758 CGTCCGGTATGTGATAGGCCAGTTTAGGATTATTCTAGTTCAGGAAAAGACCTTTTCAGGAGTTT
194 CGTCCGGCATGTGATAGGCCAGTTTAGGATTATTCGAGTTCAGGAAAAGACCTTTTCAGGAGTTT
* *
48823 TGGAGAAATCACCTCGAATAACCAAGCTTTTGAAGCTTTCAAGTCAATAATCCGTTAAACAAATG
259 TGGAGAAATCACCTCGAATAAACAAGCTTTTGAAGCTTTCAAGTCAATAATCCGTCAAACAAATG
* *
48888 AATGGAGGGCTTTAAACAAAGCCAACAGTTTTTTCGGGTTTACCTATTTATTTTAAATATATAAT
324 AATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTTTACCTATTTATTTTAAATATATAAT
*
48953 ACAGAACACACTCAGATAAATATAATATATTATGAAGCTGATTTTCAGTGAGTTTTTGTCACATC
389 ACAGAACACACTCAGATAAATATAATATATTATAAAGCTGATTTTCAGTGAGTTTTTGTCACATC
49018 TTTTTATTTCTTGCTCAGCAGAGTATTGCTGGGATTGCTAGATCTTATGTTCTTGATCATTAAAA
454 TTTTTATTTCTTGCTCAGCAGAGTATTGCTGGGATTGCTAGATCTTATGTTCTTGATCATTAAAA
*
49083 TTTTAATCATTAAAATTTTCTCACCTT-TGTAGGTTCTCCCCATAATCCTCAGACTGTATCTTTC
1 TTTTAATCATTAAAATTTTCTCACCTTGTGCAGGTTCTCCCCATAATCCTCAGACTGTATCTTTC
*
49147 TTGGGATTGCTAGA-T-CTTATGTTCTTGACAATGCATCGGACTCCAGGGATACTCCTGCTTCAT
66 TTGGAATTGCTAGATTCCTTATGTTCTTGACAATGCATCGGACTCCAGGGATACTCCTGCTTCAT
* *
49210 TGCTTAAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATGTTACAGCG
131 TGCCTAAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATATTACAGCG
*
49275 TCCGGCATGTGATAGGCCAGTTTAGGATTATTCGAGTTCAGGGAAAATACCTTTTCAGGAGTTTT
196 TCCGGCATGTGATAGGCCAGTTTAGGATTATTCGAGTTCA-GGAAAAGACCTTTTCAGGAGTTTT
*
49340 GGAGAAATCACCTCGAATAAACAAGCTTTTGAAGCTTTCAAGTTAATAATCCGTCAAA-ATAATG
260 GGAGAAATCACCTCGAATAAACAAGCTTTTGAAGCTTTCAAGTCAATAATCCGTCAAACA-AATG
*
49404 AATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTTTACCTATTTATTTTAAATATATAGT
324 AATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTTTACCTATTTATTTTAAATATATAAT
**
49469 ATGGAACACACTCAGATAAATATAATATATTATAAAGCTGATTTT
389 ACAGAACACACTCAGATAAATATAATATATTATAAAGCTGATTTT
49514 GTCTTTGCCC
Statistics
Matches: 407, Mismatches: 22, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
515 146 0.36
516 187 0.46
519 48 0.12
520 26 0.06
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (518 bp):
TTTTAATCATTAAAATTTTCTCACCTTGTGCAGGTTCTCCCCATAATCCTCAGACTGTATCTTTC
TTGGAATTGCTAGATTCCTTATGTTCTTGACAATGCATCGGACTCCAGGGATACTCCTGCTTCAT
TGCCTAAAAAGGGTAAAGAGTTTTCTATTTACCTTGTCCCACTCAGTTTTGATGATATTACAGCG
TCCGGCATGTGATAGGCCAGTTTAGGATTATTCGAGTTCAGGAAAAGACCTTTTCAGGAGTTTTG
GAGAAATCACCTCGAATAAACAAGCTTTTGAAGCTTTCAAGTCAATAATCCGTCAAACAAATGAA
TGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTTTACCTATTTATTTTAAATATATAATAC
AGAACACACTCAGATAAATATAATATATTATAAAGCTGATTTTCAGTGAGTTTTTGTCACATCTT
TTTATTTCTTGCTCAGCAGAGTATTGCTGGGATTGCTAGATCTTATGTTCTTGATCATTAAAA
Found at i:50491 original size:24 final size:24
Alignment explanation
Indices: 50455--50526 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
50445 TTGAAACCAG
*
50455 TTCCCCAGCTCCTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
* *
50479 TTCCACTGTTCCTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
*
50503 TTCCACAGCTCTTCTCTTCACCCT
1 TTCCACAGCTCCTCTCTTCACCCT
50527 ATCGATTGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.10, C:0.49, G:0.04, T:0.38
Consensus pattern (24 bp):
TTCCACAGCTCCTCTCTTCACCCT
Found at i:52993 original size:34 final size:34
Alignment explanation
Indices: 52935--53000 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
52925 GAAACACTAG
*
52935 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGAAAATCATTTTAC-GAAAAGT
*
52970 AAAATATTTTTCA-AAAATCATTTTACGAAAA
1 AAAATATTTTCCAGAAAATCATTTTACGAAAA
53001 ATATTTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (34 bp):
AAAATATTTTCCAGAAAATCATTTTACGAAAAGT
Found at i:53000 original size:14 final size:13
Alignment explanation
Indices: 52970--53008 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
52960 ACAGAAAAGT
*
52970 AAAATATTTTTCA
1 AAAATATTTTACA
52983 AAAATCATTTTACGA
1 AAAAT-ATTTTAC-A
52998 AAAATATTTTA
1 AAAATATTTTA
53009 GTGCCTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 5 0.22
14 12 0.52
15 6 0.26
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (13 bp):
AAAATATTTTACA
Found at i:54378 original size:78 final size:78
Alignment explanation
Indices: 54278--54428 Score: 230
Period size: 78 Copynumber: 1.9 Consensus size: 78
54268 CTCATTTTCC
* *
54278 ACCATTAAACCATGATCCCTTGATCTCACCAACTGGGAGAGTCGGTGATCATGTTAATAATGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
54343 ACCATGGAGTTCG
66 ACCATGGAGTTCG
* * * * *
54356 ACCATTAAACCATGATCCCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
*
54421 ATCATGGA
66 ACCATGGA
54429 CTTTGTGTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (78 bp):
ACCATTAAACCATGATCCCTTGATCTCACCAACTAGGAGAGTCGGTGATCATGTTAATAACGATC
ACCATGGAGTTCG
Found at i:56990 original size:9 final size:9
Alignment explanation
Indices: 56976--57043 Score: 91
Period size: 9 Copynumber: 7.6 Consensus size: 9
56966 TTTGGTTAAA
56976 AATTACCCG
1 AATTACCCG
56985 AATTACCCG
1 AATTACCCG
*
56994 AATTATCCG
1 AATTACCCG
*
57003 AATTATCCG
1 AATTACCCG
**
57012 AATTAATCG
1 AATTACCCG
57021 AATTACCCG
1 AATTACCCG
*
57030 AATTACCTG
1 AATTACCCG
57039 AATTA
1 AATTA
57044 ATCGAATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTACCCG
Found at i:57014 original size:27 final size:27
Alignment explanation
Indices: 56977--57052 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
56967 TTGGTTAAAA
** *
56977 ATTACCCGAATTACCCGAATTATCCGA
1 ATTACCCGAATTAATCGAATTACCCGA
*
57004 ATTATCCGAATTAATCGAATTACCCGA
1 ATTACCCGAATTAATCGAATTACCCGA
*
57031 ATTACCTGAATTAATCGAATTA
1 ATTACCCGAATTAATCGAATTA
57053 ACCTAATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (27 bp):
ATTACCCGAATTAATCGAATTACCCGA
Found at i:57060 original size:18 final size:18
Alignment explanation
Indices: 56976--57065 Score: 67
Period size: 18 Copynumber: 4.9 Consensus size: 18
56966 TTTGGTTAAA
* **
56976 AATTACCCGAATTACCCG
1 AATTAACCGAATTAATCG
*
56994 AATTATCCGAATT-ATCCG
1 AATTAACCGAATTAAT-CG
* **
57012 AATTAATCGAATTACCCG
1 AATTAACCGAATTAATCG
57030 AATT-ACCTGAATTAATCG
1 AATTAACC-GAATTAATCG
*
57048 AATTAACCTAATTGAATC
1 AATTAACCGAATT-AATC
57066 ATACATAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
17 2 0.04
18 47 0.84
19 7 0.12
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (18 bp):
AATTAACCGAATTAATCG
Found at i:57060 original size:27 final size:26
Alignment explanation
Indices: 56976--57060 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 26
56966 TTTGGTTAAA
** *
56976 AATTACCCGAATTACCCGAATTATCCG
1 AATTA-CCGAATTAATCGAATTAACCG
*
57003 AATTATCCGAATTAATCGAATTACCCG
1 AATTA-CCGAATTAATCGAATTAACCG
*
57030 AATTACCTGAATTAATCGAATTAACCT
1 AATTACC-GAATTAATCGAATTAACCG
57057 AATT
1 AATT
57061 GAATCATACA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
26 2 0.04
27 49 0.96
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (26 bp):
AATTACCGAATTAATCGAATTAACCG
Found at i:57150 original size:18 final size:19
Alignment explanation
Indices: 57127--57165 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
57117 TTATAGAATT
* *
57127 TTATTTTTATTTTTTA-AA
1 TTATTTGTAATTTTTATAA
57145 TTATTTGTAATTTTTATAA
1 TTATTTGTAATTTTTATAA
57164 TT
1 TT
57166 GGGATGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTATTTGTAATTTTTATAA
Found at i:57532 original size:20 final size:20
Alignment explanation
Indices: 57507--57548 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
57497 CATAGCAAAA
57507 GGACATTAGTGAAATGTTGT
1 GGACATTAGTGAAATGTTGT
*
57527 GGACATTAGTGCAATGTTGT
1 GGACATTAGTGAAATGTTGT
57547 GG
1 GG
57549 TCAGCTACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (20 bp):
GGACATTAGTGAAATGTTGT
Done.