Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold537
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: 76715
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:1510 original size:2 final size:2
Alignment explanation
Indices: 1503--1570 Score: 93
Period size: 2 Copynumber: 34.5 Consensus size: 2
1493 TGTACCTTGT
* * *
1503 TA TA TA TA TA TA TA TA CA TA TA TA TG TA TA TA -A TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1544 TA TA TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1571 GATTGAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3355 original size:156 final size:156
Alignment explanation
Indices: 3079--3377 Score: 336
Period size: 156 Copynumber: 1.9 Consensus size: 156
3069 AACCTATTCT
* *
3079 TAAAGCACACCTTTGACATCAAAGTATCTCAGTGAATCTAAAGGACTTGGTTCAAAGATAAAGTT
1 TAAAGCACACCTTTGACATCAAAGCATCTCAGTGAATCTAAAAGACTTGGTTCAAAGATAAAGTT
* * ** * * *
3144 ATAAAAATGCCCTTAAGATGTACCTTGGACATGAAAATATCCCGATAATCCTAAAAAAGTCAATA
66 ATAAAAATACCCTTAAGACGTACCTTCAACATGAAAATATCCCAATAATCATAAAAAACTCAATA
3209 ATAAT-ATGAAATGACAAATAAATCCC
131 AT-ATCATGAAATGACAAATAAATCCC
* * * * * *
3235 TAAAGCACACTTTTGACATGAAAGCATCTCAGTG-ATCTTAAAAGACTTAGTTTTAAGGTTAAA-
1 TAAAGCACACCTTTGACATCAAAGCATCTCAGTGAATC-TAAAAGACTT-GGTTCAAAGATAAAG
* * * * * * *
3298 TTATTAAAATACTCTTAAGACGTACCTTCAATATGAAAGTATTCTAATAA-CTATAAAAAACTCG
64 TTATAAAAATACCCTTAAGACGTACCTTCAACATGAAAATATCCCAATAATC-ATAAAAAACTCA
3362 ATAATATCATGAAATG
128 ATAATATCATGAAATG
3378 GTAATCATAC
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
155 6 0.05
156 101 0.86
157 10 0.09
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (156 bp):
TAAAGCACACCTTTGACATCAAAGCATCTCAGTGAATCTAAAAGACTTGGTTCAAAGATAAAGTT
ATAAAAATACCCTTAAGACGTACCTTCAACATGAAAATATCCCAATAATCATAAAAAACTCAATA
ATATCATGAAATGACAAATAAATCCC
Found at i:7646 original size:24 final size:24
Alignment explanation
Indices: 7601--7648 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
7591 GAAGATTATT
*
7601 TTCTTTGAGAAATGAAGGGGCAAA
1 TTCTTTGAGAAATGAACGGGCAAA
* *
7625 TTCTTTGAGTAATGAACTGGCAAA
1 TTCTTTGAGAAATGAACGGGCAAA
7649 AAGAACCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (24 bp):
TTCTTTGAGAAATGAACGGGCAAA
Found at i:8102 original size:2 final size:2
Alignment explanation
Indices: 8095--8124 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8085 TTGTTTTTCT
8095 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
8125 AAGGTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8712 original size:2 final size:2
Alignment explanation
Indices: 8705--8741 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8695 TCTTTTGGTG
8705 TA 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 TA T
8742 CAAGTACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11267 original size:2 final size:2
Alignment explanation
Indices: 11260--11305 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
11250 TTTTGATGAG
11260 TA TA TA 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 TA TA TA TA
11301 TA TA T
1 TA TA T
11306 CAAGTACATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13368 original size:2 final size:2
Alignment explanation
Indices: 13361--13389 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13351 TTTTGGTTGC
13361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13390 CACATAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14142 original size:24 final size:24
Alignment explanation
Indices: 14097--14144 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
14087 GAAGATTATT
**
14097 TTCTTTGAGTAATAAATGGGCAAA
1 TTCTTTGAGTAATAAACAGGCAAA
*
14121 TTCTTTGAGTAATGAACAGGCAAA
1 TTCTTTGAGTAATAAACAGGCAAA
14145 AAGACCCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (24 bp):
TTCTTTGAGTAATAAACAGGCAAA
Found at i:15328 original size:2 final size:2
Alignment explanation
Indices: 15321--15345 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15311 GTTGCACAAT
15321 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 T
15346 GCATAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18002 original size:2 final size:2
Alignment explanation
Indices: 17995--18027 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
17985 TCTTTTGGTG
17995 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18028 AAGTACTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18399 original size:16 final size:16
Alignment explanation
Indices: 18378--18424 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
18368 AATATAAAAT
18378 TTTAAACTTAAAATAA
1 TTTAAACTTAAAATAA
18394 TTTAAA-TCTAAAAT-A
1 TTTAAACT-TAAAATAA
*
18409 TTTAAACTCAAAATAA
1 TTTAAACTTAAAATAA
18425 CCAAACTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (16 bp):
TTTAAACTTAAAATAA
Found at i:18413 original size:15 final size:14
Alignment explanation
Indices: 18372--18423 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 14
18362 TAAATAAATA
18372 TAAAAT-TTTAAAC
1 TAAAATATTTAAAC
18385 TTAAAATAATTTAAATC
1 -TAAAAT-ATTTAAA-C
18402 TAAAATATTTAAAC
1 TAAAATATTTAAAC
18416 TCAAAATA
1 T-AAAATA
18424 ACCAAACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.24
15 13 0.38
16 12 0.35
17 1 0.03
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAATATTTAAAC
Found at i:18416 original size:31 final size:29
Alignment explanation
Indices: 18357--18424 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 29
18347 TAAAGTTAAA
18357 TAAAATAAATAAATATAAAATTTTAAACT
1 TAAAATAAATAAATATAAAATTTTAAACT
* *
18386 TAAAATAATTTAAATCTAAAATATTTAAACT
1 TAAAATAA-ATAAATATAAAAT-TTTAAACT
*
18417 CAAAATAA
1 TAAAATAA
18425 CCAAACTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 8 0.24
30 11 0.32
31 15 0.44
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (29 bp):
TAAAATAAATAAATATAAAATTTTAAACT
Found at i:18527 original size:2 final size:2
Alignment explanation
Indices: 18520--18550 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18510 TTATTATTGC
18520 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
18551 TAGTCTTTTT
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:25193 original size:34 final size:34
Alignment explanation
Indices: 25151--25346 Score: 338
Period size: 34 Copynumber: 5.7 Consensus size: 34
25141 AATATAAAAT
*
25151 ACCTAACACACCTAACATTCTCACCAAATACATT
1 ACCTAACACACCTAACATTCTCACCAAATACATC
25185 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
25219 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
* *
25253 ACCTAATACACCTAACATTCTCACCAAATACATT
1 ACCTAACACACCTAACATTCTCACCAAATACATC
25287 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
* *
25321 ACCCAACACACCTAATATTCTTCACC
1 ACCTAACACACCTAACATTC-TCACC
25347 TAACACACTT
Statistics
Matches: 154, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
34 149 0.97
35 5 0.03
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.22
Consensus pattern (34 bp):
ACCTAACACACCTAACATTCTCACCAAATACATC
Found at i:25256 original size:25 final size:25
Alignment explanation
Indices: 25159--25258 Score: 67
Period size: 25 Copynumber: 4.3 Consensus size: 25
25149 ATACCTAACA
25159 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
* *
25184 TACCTAACA----CACCTAACATTC-T
1 CACCTAACATTCTCACC-AA-ATACAT
* *
25206 CACC-AA-ATACATCACC-TA-ACA-
1 CACCTAACATTC-TCACCAAATACAT
25227 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
25252 CACCTAA
1 CACCTAA
25259 TACACCTAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 26
0.62 0.08 0.30
Matches are distributed among these distances:
20 1 0.02
21 11 0.20
22 14 0.25
23 7 0.13
24 3 0.05
25 19 0.35
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:30097 original size:34 final size:34
Alignment explanation
Indices: 30054--30256 Score: 343
Period size: 34 Copynumber: 5.9 Consensus size: 34
30044 AATATAAAAT
30054 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
30088 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
*
30122 ACCTATCACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
* *
30156 ACCTAATACACCTAACATTCTCACCAAATACATT
1 ACCTAACACACCTAACATTCTCACCAAATACATC
30190 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
* * *
30224 ACCTAACACACCTAATATTTTTCACCTAATACA
1 ACCTAACACACCTAACA-TTCTCACCAAATACA
30257 CTTAACAAAG
Statistics
Matches: 159, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
34 146 0.92
35 13 0.08
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (34 bp):
ACCTAACACACCTAACATTCTCACCAAATACATC
Found at i:30125 original size:25 final size:25
Alignment explanation
Indices: 30096--30197 Score: 62
Period size: 22 Copynumber: 4.4 Consensus size: 25
30086 TCACCTAACA
30096 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
* *
30121 CACCT---A-TCACACCTAACATTC-T
1 CACCTAACATTCTCACC-AA-ATACAT
* *
30143 CACC-AA-ATACATCACCTAAT--A-
1 CACCTAACATTC-TCACCAAATACAT
30164 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
*
30189 TACCTAACA
1 CACCTAACA
30198 CACCTAACAT
Statistics
Matches: 57, Mismatches: 8, Indels: 24
0.64 0.09 0.27
Matches are distributed among these distances:
21 10 0.18
22 18 0.32
23 9 0.16
24 3 0.05
25 17 0.30
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:38266 original size:27 final size:27
Alignment explanation
Indices: 38201--38271 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
38191 AAACAAGCCT
* *
38201 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
38229 CCATTTTTGACAAACACAAA-ATAACTA
1 CCATTTTTGACAAACACAAAGA-AACCA
38256 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
38272 AATGGGTAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:40191 original size:21 final size:22
Alignment explanation
Indices: 40153--40198 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
40143 ATCTGTTGAA
* **
40153 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
40174 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
40196 ACT
1 ACT
40199 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:43971 original size:20 final size:20
Alignment explanation
Indices: 43946--43984 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
43936 TCATGAGTTA
43946 ATTATA-AAATTAATTTTTAT
1 ATTATATAAATT-ATTTTTAT
43966 ATTATATTAAATTATTTTT
1 ATTATA-TAAATTATTTTT
43985 GTTTAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATATAAATTATTTTTAT
Found at i:44331 original size:20 final size:20
Alignment explanation
Indices: 44299--44432 Score: 73
Period size: 20 Copynumber: 6.5 Consensus size: 20
44289 TTATATTTAA
44299 AATA-TTATA-TATTTTATT
1 AATATTTATATTATTTTATT
*
44317 AATATTTATATTA-TTAATT
1 AATATTTATATTATTTTATT
* * *
44336 TATA-TTATATAAATTTTAAT
1 AATATTTATAT-TATTTTATT
44356 -ATATTTATATCGTATTTATATT
1 AATATTTATAT--TATTT-TATT
* *
44378 ATTTATATTATATTATATT-TT
1 A-ATAT-TTATATTATTTTATT
44399 AATTATTTATATTATATTATATT
1 AA-TATTTATATTAT-TT-TATT
*
44422 TATATATTATA
1 AATAT-TTATA
44433 AAATTATATC
Statistics
Matches: 88, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
18 10 0.11
19 17 0.19
20 21 0.24
21 11 0.12
22 8 0.09
23 12 0.14
24 3 0.03
25 6 0.07
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (20 bp):
AATATTTATATTATTTTATT
Found at i:44373 original size:11 final size:9
Alignment explanation
Indices: 44300--44431 Score: 89
Period size: 9 Copynumber: 14.8 Consensus size: 9
44290 TATATTTAAA
*
44300 ATATTATAT
1 ATATTATTT
* *
44309 ATTTTATTA
1 ATATTATTT
44318 ATATTTATATT
1 ATA-TTAT-TT
*
44329 AT-TAATTT
1 ATATTATTT
*
44337 ATATTATAT
1 ATATTATTT
* *
44346 AAATT-TTA
1 ATATTATTT
44354 ATA-TATTT
1 ATATTATTT
44362 ATATCGTATTT
1 ATAT--TATTT
44373 ATATTATTT
1 ATATTATTT
44382 ATATTATATT
1 ATATTAT-TT
44392 ATA-T-TTT
1 ATATTATTT
44399 A-ATTATTT
1 ATATTATTT
44407 ATATTATATT
1 ATATTAT-TT
*
44417 ATATT-TAT
1 ATATTATTT
44425 ATATTAT
1 ATATTAT
44432 AAAATTATAT
Statistics
Matches: 96, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
6 1 0.01
7 5 0.05
8 23 0.24
9 39 0.41
10 16 0.17
11 12 0.12
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (9 bp):
ATATTATTT
Found at i:44406 original size:45 final size:44
Alignment explanation
Indices: 44313--44437 Score: 143
Period size: 45 Copynumber: 2.9 Consensus size: 44
44303 TTATATATTT
* *
44313 TATTAATATTTATATTAT-TAATTTATATTATATAAATTTTAATA
1 TATTTATA-TTATATTATATTATTTATATTATATAAATTTTAATA
*
44357 TATTTATATCGTAT-TTATATTATTTATATTATATTATATTTTAAT-
1 TATTTATAT--TATATTATATTATTTATATTATA-TAAATTTTAATA
*
44402 TATTTATATTATATTATATT-TATATATTATA-AAATT
1 TATTTATATTATATTATATTATTTATATTATATAAATT
44438 ATATCGTAGG
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
41 4 0.06
43 14 0.20
44 18 0.25
45 25 0.35
46 10 0.14
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (44 bp):
TATTTATATTATATTATATTATTTATATTATATAAATTTTAATA
Found at i:44416 original size:25 final size:25
Alignment explanation
Indices: 44308--44431 Score: 104
Period size: 25 Copynumber: 5.1 Consensus size: 25
44298 AAATATTATA
*
44308 TATTT-TATTAATATT-TATATT-AT
1 TATTTATATT-ATATTATATTTTAAT
*
44331 TAATTTATATTATA-TAAATTTTAA-
1 T-ATTTATATTATATTATATTTTAAT
**
44355 TA--TAT-TTATATCGTA-TTTATAT
1 TATTTATATTATATTATATTTTA-AT
44377 TATTTATATTATATTATATTTTAAT
1 TATTTATATTATATTATATTTTAAT
44402 TATTTATATTATATTATATTTATATAT
1 TATTTATATTATATTATATTT-TA-AT
44429 TAT
1 TAT
44432 AAAATTATAT
Statistics
Matches: 81, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
20 9 0.11
21 5 0.06
22 2 0.02
23 3 0.04
24 15 0.19
25 36 0.44
26 6 0.07
27 5 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (25 bp):
TATTTATATTATATTATATTTTAAT
Found at i:44419 original size:55 final size:53
Alignment explanation
Indices: 44263--44431 Score: 153
Period size: 49 Copynumber: 3.3 Consensus size: 53
44253 ATTTACATTT
* *
44263 TATT-TTTATATT-TTTATGTATTATGATTATATTTAAAATATTATATATTTTATTA
1 TATTATTTATATTATTTA--TATTAT-ATTATATTTAAATTATT-TATATTATATTA
* *
44318 -A-TATTTATATTATTAAT-TTATATTATA--TAAATT-TTAATA-TAT-TTA
1 TATTATTTATATTATTTATATTATATTATATTTAAATTATTTATATTATATTA
*
44363 TATCGTATTTATATTATTTATATTATATTATATTTTAATTATTTATATTATATTA
1 TAT--TATTTATATTATTTATATTATATTATATTTAAATTATTTATATTATATTA
*
44418 TATT-TATATATTAT
1 TATTATTTATATTAT
44432 AAAATTATAT
Statistics
Matches: 94, Mismatches: 8, Indels: 27
0.73 0.06 0.21
Matches are distributed among these distances:
45 3 0.03
46 3 0.03
47 3 0.03
48 2 0.02
49 20 0.21
50 10 0.11
51 6 0.06
52 18 0.19
53 8 0.09
54 12 0.13
55 9 0.10
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.61
Consensus pattern (53 bp):
TATTATTTATATTATTTATATTATATTATATTTAAATTATTTATATTATATTA
Found at i:44538 original size:18 final size:18
Alignment explanation
Indices: 44515--44549 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44505 AGTCAAAGCT
* *
44515 TTTTGATGTTTTTGATAC
1 TTTTGAAGTTTTGGATAC
44533 TTTTGAAGTTTTGGATA
1 TTTTGAAGTTTTGGATA
44550 TGGCTGAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.20, T:0.57
Consensus pattern (18 bp):
TTTTGAAGTTTTGGATAC
Found at i:44808 original size:28 final size:28
Alignment explanation
Indices: 44770--44832 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
44760 GAATGTGTTT
44770 TATATATTATAAATTATTAAAATTTATA
1 TATATATTATAAATTATTAAAATTTATA
44798 TATATATTATAAATTATTAAAATTTATA
1 TATATATTATAAATTATTAAAATTTATA
*
44826 TAGATAT
1 TATATAT
44833 GTAATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TATATATTATAAATTATTAAAATTTATA
Found at i:45511 original size:23 final size:25
Alignment explanation
Indices: 45485--45532 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
45475 AGATTTTTCC
45485 TTATGAA-TTTTATT-TAAAATATT
1 TTATGAATTTTTATTATAAAATATT
* *
45508 TTATTAATTTTTTTTATAAAATATT
1 TTATGAATTTTTATTATAAAATATT
45533 CTATCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TTATGAATTTTTATTATAAAATATT
Found at i:45980 original size:14 final size:14
Alignment explanation
Indices: 45963--46015 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
45953 ACGGGAAGAG
45963 AAAAAAAGGAAAAA
1 AAAAAAAGGAAAAA
45977 AAAAAAA-GAAAGAA
1 AAAAAAAGGAAA-AA
45991 AAAAAGAGAGAGAAAAA
1 AAAAA-A-AG-GAAAAA
46008 AGAAAAAA
1 A-AAAAAA
46016 ATTACGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 4 0.12
14 14 0.42
15 1 0.03
16 2 0.06
17 4 0.12
18 8 0.24
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAGGAAAAA
Found at i:45981 original size:13 final size:13
Alignment explanation
Indices: 45963--45996 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
45953 ACGGGAAGAG
45963 AAAAAAAGGAAAA
1 AAAAAAAGGAAAA
* *
45976 AAAAAAAAGAAAG
1 AAAAAAAGGAAAA
45989 AAAAAAAG
1 AAAAAAAG
45997 AGAGAGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGAAAA
Found at i:46075 original size:19 final size:17
Alignment explanation
Indices: 46037--46081 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
46027 GTATTATTTT
46037 TTTAT-TATTTAAAATA
1 TTTATATATTTAAAATA
46053 -TTATATATTTATATAATA
1 TTTATATATTTA-A-AATA
46071 TTTATATATTT
1 TTTATATATTT
46082 TATGTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.16
16 6 0.24
17 1 0.04
18 4 0.16
19 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATATTTAAAATA
Found at i:47774 original size:17 final size:18
Alignment explanation
Indices: 47733--47777 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
47723 AATTTAAATA
*
47733 AATAAATATTTATTTATTT
1 AATAAA-ATTTAATTATTT
47752 AATAAAATTTAATT-TTT
1 AATAAAATTTAATTATTT
*
47769 ATTAAAATT
1 AATAAAATT
47778 AGATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.46
18 7 0.29
19 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATAAAATTTAATTATTT
Found at i:47973 original size:28 final size:29
Alignment explanation
Indices: 47915--47969 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
47905 TTTAATGCAT
*
47915 AATTATTATTTAATAAAAATTATAAATTA
1 AATTATTATTTAATAAAAACTATAAATTA
* *
47944 AATTTTTA-TTAATAATAACTA-AAATT
1 AATTATTATTTAATAAAAACTATAAATT
47970 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 11 0.48
29 7 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTATTATTTAATAAAAACTATAAATTA
Found at i:52104 original size:48 final size:48
Alignment explanation
Indices: 52040--52349 Score: 416
Period size: 48 Copynumber: 6.6 Consensus size: 48
52030 TGAGAGGAGT
** * *
52040 GACAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
* *
52088 GACAATGTGGTGATTCAAGGCCAGCGACATTAAGCTAAGGG-AAAATG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
*
52135 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA-TGAAAAAGTG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAA-TG
*
52183 GACAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGG-AAAATG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
* * *
52230 TACAATGTGCTGATTCAAGGCCAGCGACATTTAGCTAATGGAAAAATG
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
* * *
52278 GATAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA--TAAAAGT-
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
* * *
52323 GCCAATATGCTGATTCAATGCCAGCGA
1 GACAATGTGCTGATTCAAGGCCAGCGA
52350 TATCGAATTT
Statistics
Matches: 234, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
45 23 0.10
46 6 0.03
47 85 0.36
48 119 0.51
49 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (48 bp):
GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAATG
Found at i:52170 original size:95 final size:94
Alignment explanation
Indices: 52040--52349 Score: 428
Period size: 95 Copynumber: 3.3 Consensus size: 94
52030 TGAGAGGAGT
** * * *
52040 GACAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGGTGATTCA
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA-GGAAAAATGGACAATGTGCTGATTCA
*
52105 AGGCCAGCGACATTAAGCTAAGGGAAAATG
65 AGGCCAGCGACATTGAGCTAAGGGAAAATG
*
52135 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATGAAAAAGTGGACAATGTGCTGATTCA
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGAAAAA-TGGACAATGTGCTGATTCA
*
52200 AGGCCAACGACATTGAGCTAAGGGAAAATG
65 AGGCCAGCGACATTGAGCTAAGGGAAAATG
* * *
52230 TACAATGTGCTGATTCAAGGCCAGCGACATTTAGCTAATGGAAAAATGGATAATGTGCTGATTCA
1 GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA-GGAAAAATGGACAATGTGCTGATTCA
*
52295 AGGCCAGCGACATTGAGCTAA--TAAAA-G
65 AGGCCAGCGACATTGAGCTAAGGGAAAATG
* * *
52322 TGCCAATATGCTGATTCAATGCCAGCGA
1 -GACAATGTGCTGATTCAAGGCCAGCGA
52350 TATCGAATTT
Statistics
Matches: 194, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
92 1 0.01
93 27 0.14
94 6 0.03
95 154 0.79
96 6 0.03
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (94 bp):
GACAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAAGGAAAAATGGACAATGTGCTGATTCAA
GGCCAGCGACATTGAGCTAAGGGAAAATG
Found at i:52298 original size:143 final size:140
Alignment explanation
Indices: 52037--52355 Score: 478
Period size: 143 Copynumber: 2.3 Consensus size: 140
52027 AGATGAGAGG
** *
52037 AGTGACAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGGTGAT
1 AGTGACAATGTGCTGATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGCTGAT
*
52102 TCAAGGCCAGCGACATTAAGCTAAGGGAAAATGGACAATGTGCTGATTCAAGGCCAGCGACATTG
66 TCAAGGCCAGCGACATTAAGCTAAGGAAAAATGGACAATGTGCTGATTCAAGGCCAGCGACATTG
52167 AGCTAATGAAAA
131 AGCTAAT--AAA
* *
52179 AGTGGACAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGG-AAAATGTACAATGTGCTGA
1 AGT-GACAATGTGCTGATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGCTGA
* *
52243 TTCAAGGCCAGCGACATTTAGCTAATGGAAAAATGGATAATGTGCTGATTCAAGGCCAGCGACAT
65 TTCAAGGCCAGCGACATTAAGCTAA-GGAAAAATGGACAATGTGCTGATTCAAGGCCAGCGACAT
52308 TGAGCTAATAAA
129 TGAGCTAATAAA
* * * * *
52320 AGTGCCAATATGCTGATTCAATGCCAGCGATATCGA
1 AGTGACAATGTGCTGATTCAAGGCCAACGACATCGA
52356 ATTTTAAGAT
Statistics
Matches: 161, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
140 27 0.17
141 6 0.04
142 44 0.27
143 84 0.52
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (140 bp):
AGTGACAATGTGCTGATTCAAGGCCAACGACATCGAGCTAAGGGAAAAATGGACAATGTGCTGAT
TCAAGGCCAGCGACATTAAGCTAAGGAAAAATGGACAATGTGCTGATTCAAGGCCAGCGACATTG
AGCTAATAAA
Found at i:52477 original size:28 final size:28
Alignment explanation
Indices: 52420--53428 Score: 305
Period size: 32 Copynumber: 33.1 Consensus size: 28
52410 GCTTTTAAAA
* *
52420 AAAAGGTGCCACTAACTTCTGTGGGCTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
* *
52450 AAGAGATGCCACT-ACCTTGTGGGTTTTG
1 AAAAGATGCCACTGA-CTTGTGGGCTTTG
*
52478 AAAAGATGCCACTAACTTGTGGGCTTT-
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
52505 AGAAGGATGCCACTGACTTGTCGGCTTTG
1 A-AAAGATGCCACTGACTTGTGGGCTTTG
* * *
52534 AAAAGTTGCCACTGACTCGTCGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
52562 AAAAGTTGCCACTGACTTGTGGGCTTGG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
52590 AAAAGATGCCACCGACTTGTGTGGGTTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
* * ** *
52620 AAATGGGTTGCCACCAACTTGTGTGGGCTATG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* ** *
52652 AAATGAGTTGCCACCAACTTGTGTGGGCATTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * *
52684 AAAGGATACCACTGACTTGTGGGCTTTA
1 AAAAGATGCCACTGACTTGTGGGCTTTG
*
52712 AAAAGATGCCACCGACTTGTGTGGGCTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
** * * ** *
52742 ACATGGGCTACCACCAACTTGTGTGGGCTATG
1 A-A-AAGATGCCACTGAC-T-TGTGGGCTTTG
* ** *
52774 AAATGAGTTGCCACCAACTTGTGTGGGCATTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
*
52806 -AAAGGTCGCCACTGACTTGTGGGCTTTG
1 AAAAGAT-GCCACTGACTTGTGGGCTTTG
* * *
52834 AAAGGGTGCCACTGTCTTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
*
52862 AAAAGATGCCACCGACTTGTATGGGCTTTG
1 AAAAGATGCCACTGACTTG--TGGGCTTTG
* * * **
52892 AAATGGGTTGTCACCAACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* **
52924 AAATGAGTTGCCACCAACTTGTGTGGACTTTG
1 AAA--AGATGCCACTGACTTGTG-GG-CTTTG
* ** *
52956 AAATGAGTTGCCACCAACTTGTGTAGGCTTTC
1 AAA--AGATGCCACTGACTTGTG--GGCTTTG
* * ** *
52988 AAATGGGTTGCCACCAACTTGTGTGGGCTTTC
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * ** *
53020 AAATAGGTTGTCACCAAATTGTGTGGGCTTTG
1 AAA-A-GATGCCA-CTGACT-TGTGGGCTTTG
* ** *
53052 AAATAGGTTGCCACCAACTTATGTGGGCTTTC
1 AAA-A-GATGCCACTGAC-T-TGTGGGCTTTG
* *
53084 AAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * *
53116 AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
*
53144 AAAAGATGCCACCGACTTGTGTGGGCTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
* * **
53174 AAATGGGTTGCCACCAACTTGTGTGGACTTTG
1 AAA--AGATGCCACTGACTTGTG-GG-CTTTG
* * *
53206 AAATGAGTTGCAACCGACTTGTATGGGCTTTG
1 AAA--AGATGCCACTGACTTG--TGGGCTTTG
* * **
53238 AAATGGGTTGCCACCAACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * ** *
53270 AAATATGTTACCACCAACTTGTGTGGGCTTTC
1 AAA-A-GATGCCACTGAC-T-TGTGGGCTTTG
* *
53302 AAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
* * *
53334 AAAGGGTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
* * **
53364 AAAGGGTGCCACCCACTTGTGTAGGCTTTG
1 AAAAGATGCCACTGACTTGTG--GGCTTTG
* * *
53394 AAATGGGTTGCCACTAACTTGTGTGGGCTTTG
1 AAA--AGATGCCACTGAC-T-TGTGGGCTTTG
53426 AAA
1 AAA
53429 TGAGTTGCCA
Statistics
Matches: 816, Mismatches: 114, Indels: 96
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.00
28 213 0.26
29 19 0.02
30 143 0.18
31 13 0.02
32 400 0.49
33 13 0.02
34 14 0.02
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (28 bp):
AAAAGATGCCACTGACTTGTGGGCTTTG
Found at i:52516 original size:56 final size:55
Alignment explanation
Indices: 52420--52894 Score: 288
Period size: 56 Copynumber: 8.1 Consensus size: 55
52410 GCTTTTAAAA
* *
52420 AAAAGGTGCCACTAACTTCTGTGGGCTTTGAAGAGATGCCACT-ACCTTGTGGGTTTTG
1 AAAAGATGCCACTAAC-T-TGTGGGCTTTGAAG-GATGCCACTGA-CTTGTGGGCTTTG
*
52478 AAAAGATGCCACTAACTTGTGGGCTTTAGAAGGATGCCACTGACTTGTCGGCTTTG
1 AAAAGATGCCACTAACTTGTGGGCTTT-GAAGGATGCCACTGACTTGTGGGCTTTG
* * * * * * *
52534 AAAAGTTGCCACTGACTCGTCGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTTGG
1 AAAAGATGCCACTAACTTGTGGGCTTTG-AAGGATGCCACTGACTTGTGGGCTTTG
** * * ** *
52590 AAAAGATGCCACCGACTTGTGTGGGTTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTATG
1 AAAAGATGCCACTAAC-T-TGTGGGCTTTG-AA--GGATGCCACTGAC-T-TGTGGGCTTTG
* * * * *
52652 AAATGAGTTGCCACCAACTTGTGTGGGCATTGAAAGGATACCACTGACTTGTGGGCTTTA
1 AAA--AGATGCCACTAAC-T-TGTGGGCTTTG-AAGGATGCCACTGACTTGTGGGCTTTG
** * * ** *
52712 AAAAGATGCCACCGACTTGTGTGGGCTTTGACATGGGCTACCACCAACTTGTGTGGGCTATG
1 AAAAGATGCCACTAAC-T-TGTGGGCTTTGA-A--GGATGCCACTGAC-T-TGTGGGCTTTG
* * *
52774 AAATGAGTTGCCACCAACTTGTGTGGGCATTGAAAGG-TCGCCACTGACTTGTGGGCTTTG
1 AAA--AGATGCCACTAAC-T-TGTGGGCTTTG-AAGGAT-GCCACTGACTTGTGGGCTTTG
* * ** * *
52834 AAAGGGTGCCACTGTCTTGTGGGCTTTGAAAAGATGCCACCGACTTGTATGGGCTTTG
1 AAAAGATGCCACTAACTTGTGGGCTTTG-AAGGATGCCACTGACTTG--TGGGCTTTG
52892 AAA
1 AAA
52895 TGGGTTGTCA
Statistics
Matches: 340, Mismatches: 54, Indels: 46
0.77 0.12 0.10
Matches are distributed among these distances:
55 1 0.00
56 115 0.34
57 10 0.03
58 71 0.21
60 45 0.13
61 5 0.01
62 41 0.12
64 51 0.15
65 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (55 bp):
AAAAGATGCCACTAACTTGTGGGCTTTGAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:52562 original size:84 final size:84
Alignment explanation
Indices: 52443--52609 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 84
52433 AACTTCTGTG
* * * *
52443 GGCTTTGAAGAGATGCCACTACCTTGTGGGTTTTGAAAAGATGCCACTAACTTGTGGGCTTTAG-
1 GGCTTTGAAAAGATGCCACTACCTCGTCGGCTTTGAAAAGATGCCACTAACTTGTGGGC-TTAGA
* *
52507 AAGGATGCCACTGACTTGTC
65 AAAGATGCCACCGACTTGTC
* * * *
52527 GGCTTTGAAAAGTTGCCACTGA-CTCGTCGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTTGGA
1 GGCTTTGAAAAGATGCCACT-ACCTCGTCGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTAGA
52591 AAAGATGCCACCGACTTGT
65 AAAGATGCCACCGACTTGT
52610 GTGGGTTTTG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
83 3 0.04
84 67 0.94
85 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (84 bp):
GGCTTTGAAAAGATGCCACTACCTCGTCGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTAGAA
AAGATGCCACCGACTTGTC
Found at i:52640 original size:32 final size:32
Alignment explanation
Indices: 52596--53440 Score: 932
Period size: 32 Copynumber: 27.2 Consensus size: 32
52586 TTGGAAAAGA
* *
52596 TGCCACCGACTTGTGTGGGTTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
52628 TGCCACCAACTTGTGTGGGCTATGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
52660 TGCCACCAACTTGTGTGGGCATTGAAA--GGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* ** ** *
52690 TACCACTGAC-T-TGTGGGCTTT-AAA-AAGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
52718 TGCCACCGACTTGTGTGGGCTTTGACATGGGC
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
52750 TACCACCAACTTGTGTGGGCTATGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
52782 TGCCACCAACTTGTGTGGGCATTGAAA--GGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* **
52812 CGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*** * *
52840 TGCCACTGTC-T-TGTGGGCTTTGAAA--AGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
52868 TGCCACCGACTTGTATGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
52900 TGTCACCAACTTGTGTGGGCTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
52932 TGCCACCAACTTGTGTGGACTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
52964 TGCCACCAACTTGTGTAGGCTTTCAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
52996 TGCCACCAACTTGTGTGGGCTTTCAAATAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
53028 TGTCACCAAATTGTGTGGGCTTTGAAATAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
53060 TGCCACCAACTTATGTGGGCTTTCAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
53092 TGCCACCGACTTGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
53122 TGCCACTAAC-T-TGTGGGCTTTGAAA--AGA
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
53150 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
53182 TGCCACCAACTTGTGTGGACTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
53214 TGCAACCGACTTGTATGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
**
53246 TGCCACCAACTTGTGTGGGCTTTGAAATATGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* * *
53278 TACCACCAACTTGTGTGGGCTTTCAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
53310 TGCCACCGACTTGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
*
53340 TGCCACCGACTTGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
53370 TGCCACCCACTTGTGTAGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
* *
53402 TGCCACTAACTTGTGTGGGCTTTGAAATGAGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
53434 TGCCACC
1 TGCCACC
53441 GATGAATAAA
Statistics
Matches: 694, Mismatches: 101, Indels: 36
0.84 0.12 0.04
Matches are distributed among these distances:
27 5 0.01
28 85 0.12
29 8 0.01
30 117 0.17
31 9 0.01
32 470 0.68
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTGAAATGGGT
Found at i:64245 original size:2 final size:2
Alignment explanation
Indices: 64238--64273 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
64228 TTTATGTAAT
*
64238 TA TA TA TA TA TA TA TA TA AA 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
64274 CACCTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:66658 original size:18 final size:17
Alignment explanation
Indices: 66631--66664 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
66621 TTAAAAAGTT
66631 AAAAAATAATAATTTTA
1 AAAAAATAATAATTTTA
*
66648 AAAATAATAATTATTTT
1 AAAA-AATAATAATTTT
66665 TAATATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAAATAATAATTTTA
Found at i:67893 original size:24 final size:25
Alignment explanation
Indices: 67847--67894 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
67837 CTAAATTATT
*
67847 ATTTAATAATTAATAATATATTTAA
1 ATTTAATAATTAATAATAAATTTAA
* *
67872 ATTTAA-ATTTAATTATAAATTTA
1 ATTTAATAATTAATAATAAATTTA
67895 TATAAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTAATAATTAATAATAAATTTAA
Found at i:67909 original size:12 final size:11
Alignment explanation
Indices: 67856--67912 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
67846 TATTTAATAA
*
67856 TTAATAATATAT
1 TTAAT-ATAAAT
*
67868 TTAAATTTAAAT
1 TT-AATATAAAT
67880 TTAATTATAAAT
1 TTAA-TATAAAT
67892 TT-ATATAAAT
1 TTAATATAAAT
67902 ATTAATATAAA
1 -TTAATATAAA
67913 AATAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 23 0.61
13 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAATATAAAT
Found at i:67933 original size:29 final size:29
Alignment explanation
Indices: 67901--67979 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
67891 TTTATATAAA
*
67901 TATTAATATAAAAATAAAAATATTATTTT
1 TATTAATATAAAAATAAAAATATTAATTT
* *
67930 TATT-ATTTATAAATAATAAATATTAATTT
1 TATTAATATAAAAATAA-AAATATTAATTT
* *
67959 T-TGAATAAAAAATATAAAAAT
1 TATTAATATAAAA-ATAAAAAT
67980 TTTTAAACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
28 11 0.28
29 25 0.62
30 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
TATTAATATAAAAATAAAAATATTAATTT
Found at i:69209 original size:22 final size:22
Alignment explanation
Indices: 69179--69223 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
69169 TAAAATATTT
*
69179 AAATTTAAAT-TTAATTATAAAA
1 AAATATAAATATTAA-TATAAAA
69201 AAATATAAATATTAATATAAAA
1 AAATATAAATATTAATATAAAA
69223 A
1 A
69224 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATATAAATATTAATATAAAA
Found at i:69838 original size:2 final size:2
Alignment explanation
Indices: 69831--69857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69821 ATTGAATTGC
69831 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
69858 AAGAGAAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.