Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1107
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: 72560
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:3617 original size:3 final size:3
Alignment explanation
Indices: 3611--3647 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3601 AAAAATTTGG
*
3611 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3648 TGAGCATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4072 original size:23 final size:22
Alignment explanation
Indices: 4031--4081 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
4021 TTACATAATA
** *
4031 AAAATAAATGAAATTAAAATAAC
1 AAAA-AAATGAAAAAAAAACAAC
4054 ATAAAAAATGAAAAAAAAACAAC
1 A-AAAAAATGAAAAAAAAACAAC
4077 AAAAA
1 AAAAA
4082 CTTAATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.17
23 17 0.71
24 3 0.12
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (22 bp):
AAAAAAATGAAAAAAAAACAAC
Found at i:4738 original size:12 final size:12
Alignment explanation
Indices: 4717--4741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4707 TCATTTTTCT
4717 TTTTTTTTTCCC
1 TTTTTTTTTCCC
4729 TTTTTTTTTCCC
1 TTTTTTTTTCCC
4741 T
1 T
4742 CTTTCTCTTT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTCCC
Found at i:13124 original size:43 final size:42
Alignment explanation
Indices: 13077--13211 Score: 111
Period size: 43 Copynumber: 3.2 Consensus size: 42
13067 AACCATGAAA
13077 TGTATCGATAGATACAATTGGTAGTAGCTACCTTACCACTGTT
1 TGTATCGATAGATACAATTGGTAGTAGCTACC-TACCACTGTT
* * * * **
13120 TGTATCGATACATGTTC-ATT-GTA-TCGATA-C-ACCA-TGAAA
1 TGTATCGATAGA--TACAATTGGTAGTAGCTACCTACCACTG-TT
* *
13159 TGTATCGATAGATACAATCGGCAGTAGCTACCCTACCACTGTT
1 TGTATCGATAGATACAATTGGTAGTAGCTA-CCTACCACTGTT
13202 TGTATCGATA
1 TGTATCGATA
13212 CATGGTTAAT
Statistics
Matches: 68, Mismatches: 14, Indels: 20
0.67 0.14 0.20
Matches are distributed among these distances:
37 2 0.03
38 4 0.06
39 17 0.25
40 4 0.06
41 1 0.01
42 5 0.07
43 28 0.41
44 5 0.07
45 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (42 bp):
TGTATCGATAGATACAATTGGTAGTAGCTACCTACCACTGTT
Found at i:13163 original size:39 final size:39
Alignment explanation
Indices: 13042--13168 Score: 107
Period size: 39 Copynumber: 3.2 Consensus size: 39
13032 GATAAATTGT
*
13042 TCGATACATGTTCATTGTATCGATAAACCATGAAATGTA
1 TCGATACATGTTCATTGTATCGATACACCATGAAATGTA
* * * * **
13081 TCGATAGA--TACAATTGGTAGTAGCTACCTTACCACTG-TTTGTA
1 TCGATACATGTTC-ATT-GTA-TCGATA-C--ACCA-TGAAATGTA
13124 TCGATACATGTTCATTGTATCGATACACCATGAAATGTA
1 TCGATACATGTTCATTGTATCGATACACCATGAAATGTA
13163 TCGATA
1 TCGATA
13169 GATACAATCG
Statistics
Matches: 65, Mismatches: 13, Indels: 20
0.66 0.13 0.20
Matches are distributed among these distances:
37 2 0.03
38 5 0.08
39 24 0.37
40 4 0.06
41 1 0.02
42 4 0.06
43 18 0.28
44 5 0.08
45 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (39 bp):
TCGATACATGTTCATTGTATCGATACACCATGAAATGTA
Found at i:13185 original size:82 final size:82
Alignment explanation
Indices: 13038--13393 Score: 376
Period size: 82 Copynumber: 4.4 Consensus size: 82
13028 TATCGATAAA
* *
13038 TTGT-TCGATACATGTTCATTGTATCGATAAACCATGAAATGTATCGATAGATACAATTGGTAGT
1 TTGTATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGATACAATTGGCAGT
*
13102 AGCTACCTTACCACTGT
66 AGCTACCCTACCACTGT
*
13119 TTGTATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGATACAATCGGCAGT
1 TTGTATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGATACAATTGGCAGT
13184 AGCTACCCTACCACTGT
66 AGCTACCCTACCACTGT
* * * * * * *
13201 TTGTATCGATACATGGTTAATTGTATCGATACA--TTGAGCCCAACG-A-CTATAAATTTCAAAT
1 TTGTATCGATACAT-GTTCATTGTATCGATACACCATGA----AATGTATCGATAGA-TACAATT
* *
13262 -GCA-T-G-TA-TCGA-CACAT-T
60 GGCAGTAGCTACCCTACCAC-TGT
* * *
13279 ATGAATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGACACAATTGGCAGT
1 TTGTATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGATACAATTGGCAGT
* *
13344 AGCTACCCTATCATTGT
66 AGCTACCCTACCACTGT
* *
13361 TTGTATCGATACATGGTTAATTGTACCGATACA
1 TTGTATCGATACAT-GTTCATTGTATCGATACA
13394 TTGAGCTCAA
Statistics
Matches: 224, Mismatches: 31, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
75 3 0.01
76 5 0.02
77 25 0.11
78 17 0.08
79 7 0.03
80 4 0.02
81 11 0.05
82 103 0.46
83 41 0.18
84 5 0.02
85 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (82 bp):
TTGTATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGATACAATTGGCAGT
AGCTACCCTACCACTGT
Found at i:13310 original size:160 final size:160
Alignment explanation
Indices: 13123--13432 Score: 530
Period size: 160 Copynumber: 1.9 Consensus size: 160
13113 CACTGTTTGT
*
13123 ATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGATACAATCGGCAGTAGCT
1 ATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGACACAATCGGCAGTAGCT
*
13188 ACCCTACCACTGTTTGTATCGATACATGGTTAATTGTATCGATACATTGAGCCCAACGACTATAA
66 ACCCTACCACTGTTTGTATCGATACATGGTTAATTGTACCGATACATTGAGCCCAACGACTATAA
*
13253 ATTTCAAATGCATGTATCGACACATTATGA
131 ATTTCAAATGCATGCATCGACACATTATGA
*
13283 ATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGACACAATTGGCAGTAGCT
1 ATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGACACAATCGGCAGTAGCT
* * * **
13348 ACCCTATCATTGTTTGTATCGATACATGGTTAATTGTACCGATACATTGAGCTCAACGGTTATAA
66 ACCCTACCACTGTTTGTATCGATACATGGTTAATTGTACCGATACATTGAGCCCAACGACTATAA
*
13413 ATTTTAAATGCATGCATCGA
131 ATTTCAAATGCATGCATCGA
13433 TACTTTATCA
Statistics
Matches: 140, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
160 140 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (160 bp):
ATCGATACATGTTCATTGTATCGATACACCATGAAATGTATCGATAGACACAATCGGCAGTAGCT
ACCCTACCACTGTTTGTATCGATACATGGTTAATTGTACCGATACATTGAGCCCAACGACTATAA
ATTTCAAATGCATGCATCGACACATTATGA
Found at i:18044 original size:17 final size:16
Alignment explanation
Indices: 17994--18044 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
17984 AAAGGCTTTC
17994 AAAGTTTTTAATTAAA
1 AAAGTTTTTAATTAAA
* *
18010 AAAGGTTTTAATAGAAA
1 AAAGTTTTTAAT-TAAA
*
18027 AAATGTTTTTTATTAAA
1 AAA-GTTTTTAATTAAA
18044 A
1 A
18045 CAAAAGGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 11 0.39
17 10 0.36
18 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (16 bp):
AAAGTTTTTAATTAAA
Found at i:19739 original size:15 final size:15
Alignment explanation
Indices: 19719--19748 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19709 TAGGTTCTAA
*
19719 AAATCATATTCGTAT
1 AAATCACATTCGTAT
19734 AAATCACATTCGTAT
1 AAATCACATTCGTAT
19749 TTCAAAATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (15 bp):
AAATCACATTCGTAT
Found at i:22099 original size:159 final size:161
Alignment explanation
Indices: 21810--22126 Score: 453
Period size: 159 Copynumber: 2.0 Consensus size: 161
21800 TATTGTATCG
* * **
21810 ATACATGTTTATTGTATCGATACACCATGAAATGTATCGATAGATACAACTAGCAATAGCTATGC
1 ATACATGTTCATTGCATCGATACACCATGAAATGTATCGATAGATACAACTAGCAATAGCTACCC
* * *
21875 TATCACTGTTTGTATCGGTACATGGTTAATTATATCGATACATTGAGTCCAATAGCTATAAATTT
66 TACCACTGTTTGTATCGATACATGGTTAATTATATCGATACATTGAGTCCAACAGCTATAAATTT
21940 CAAATG-A-TGTATCGATACATTATGAGTCA
131 CAAATGCAGTGTATCGATACATTATGAGTCA
* * *
21969 ATACATGTTCATTGCATCGATACACCATGAAATGTATCGATAGTTACAA-TCGGCAGTAGCTACC
1 ATACATGTTCATTGCATCGATACACCATGAAATGTATCGATAGATACAACT-AGCAATAGCTACC
* * *
22033 CTACCACTGTTTGTATCGATACATTGTTAATTTTATCGATACATTGAG-CCTAACGGCTATAAAT
65 CTACCACTGTTTGTATCGATACATGGTTAATTATATCGATACATTGAGTCC-AACAGCTATAAAT
*
22097 TTCAAATGCATGTGTATCGATATATTATGA
129 TTCAAATGCA-GTGTATCGATACATTATGA
22127 ATTGTATCGA
Statistics
Matches: 139, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
158 3 0.02
159 118 0.85
160 1 0.01
162 17 0.12
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (161 bp):
ATACATGTTCATTGCATCGATACACCATGAAATGTATCGATAGATACAACTAGCAATAGCTACCC
TACCACTGTTTGTATCGATACATGGTTAATTATATCGATACATTGAGTCCAACAGCTATAAATTT
CAAATGCAGTGTATCGATACATTATGAGTCA
Found at i:23511 original size:12 final size:11
Alignment explanation
Indices: 23494--23533 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
23484 CTTAAGCAAA
23494 CTTTTCCTTTT
1 CTTTTCCTTTT
23505 CCTTTTCCCTTTT
1 -CTTTT-CCTTTT
*
23518 CTTTTCTTTTT
1 CTTTTCCTTTT
23529 CTTTT
1 CTTTT
23534 TTGTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.38
12 10 0.38
13 6 0.23
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTTTCCTTTT
Found at i:23523 original size:18 final size:19
Alignment explanation
Indices: 23494--23529 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
23484 CTTAAGCAAA
23494 CTTTTCCTTTTCCTTTTCC
1 CTTTTCCTTTTCCTTTTCC
*
23513 CTTTT-CTTTTCTTTTTC
1 CTTTTCCTTTTCCTTTTC
23530 TTTTTTGTTT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
CTTTTCCTTTTCCTTTTCC
Found at i:23534 original size:12 final size:12
Alignment explanation
Indices: 23494--23533 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
23484 CTTAAGCAAA
*
23494 CTTTTCCTTTTC
1 CTTTTCCTTTTT
*
23506 CTTTTCCCTTTT
1 CTTTTCCTTTTT
23518 CTTTT-CTTTTT
1 CTTTTCCTTTTT
23529 CTTTT
1 CTTTT
23534 TTGTTTGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTCCTTTTT
Found at i:26667 original size:43 final size:43
Alignment explanation
Indices: 26618--26699 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
26608 TACAAAAAAA
* * * *
26618 AAGAAAAAAATAAATATGCATAAACTAA-AAGTTAACAATGCTT
1 AAGAAAAAAACAAACATGAAGAAACTAATAA-TTAACAATGCTT
26661 AAGAAAAAAACAAACATGAAGAAACTAATAATTAACAAT
1 AAGAAAAAAACAAACATGAAGAAACTAATAATTAACAAT
26700 ACTTTACTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 32 0.94
44 2 0.06
ACGTcount: A:0.62, C:0.10, G:0.09, T:0.20
Consensus pattern (43 bp):
AAGAAAAAAACAAACATGAAGAAACTAATAATTAACAATGCTT
Found at i:28072 original size:52 final size:52
Alignment explanation
Indices: 27958--28081 Score: 142
Period size: 52 Copynumber: 2.4 Consensus size: 52
27948 TGGAGATGGT
*
27958 GGGTTGGAGTATCCCTGAAGATAAAAAATTCAGTATTTTGGAAACAAAAATA
1 GGGTTGGAGTATCCCTGAAGATAAAAAATTCAGTATTTTGGAAACAAAAACA
* * * ** * ** *
28010 GGATTGGAGTATCCTTGAAGATGAAAAATTTGGTGTTTTGGAAGTAAAAACG
1 GGGTTGGAGTATCCCTGAAGATAAAAAATTCAGTATTTTGGAAACAAAAACA
*
28062 GGGTTAGAGTATCCCT-AAGA
1 GGGTTGGAGTATCCCTGAAGA
28082 GATGGTGGGG
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 4 0.07
52 55 0.93
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (52 bp):
GGGTTGGAGTATCCCTGAAGATAAAAAATTCAGTATTTTGGAAACAAAAACA
Found at i:28446 original size:173 final size:168
Alignment explanation
Indices: 28016--28593 Score: 556
Period size: 173 Copynumber: 3.4 Consensus size: 168
28006 AATAGGATTG
** * * *
28016 GAGTATCCTTGAAGATGAAAAATTTGGTGTTTTGGAAGTAAAAACGGGGTTAGAGTAT-CCCTAA
1 GAGTATCCCCGAAGAT-AAAAATTTGGTGTTTTGGAAGTAAAAAAGGGGTTGGAGTATCCCCTCA
*
28080 GAGATGGTGGGGTTGGAGTATCCCTGAAGATGACAACTTGACATTTTCATAAATTGAAATTTAGT
65 GAGATGGTGGGGTTGGAGTAT-CCTGAAGATGACAA-TT-TCATTTTCATAAATTGAAATTTAGT
* * * * *
28145 GTAAAAAC-GAGGTTGGGTATCCCCTCAGATATGGTGGGGTTG
127 GTAAAAACAG-GGTTGAGTATCCTCTCAGAGATGATGGGGTTA
* * * * * * * * ** *
28187 GAGTGTCCTCGGAGATGAAAATTTTGGTGTTTTGCAAGTAAAGACGAGGTTGGAGTATTACCTCG
1 GAGTATCCCCGAAGAT-AAAAATTTGGTGTTTTGGAAGTAAAAAAGGGGTTGGAGTATCCCCTCA
* *
28252 GAGATGGTGGGGTTGGAGTATCCTAGAAGATCACAATTTCATGTTCTCATAAATTGAATTTTAGT
65 GAGATGGTGGGGTTGGAGTATCCT-GAAGATGACAATTTCAT-TT-TCATAAATTGAAATTTAGT
*
28317 GTAAAAACAGGGTTAAAGTATCCTCTCAGAGATGATGGGGTTA
127 GTAAAAACAGGGTT-GAGTATCCTCTCAGAGATGATGGGGTTA
* * * * *
28360 GAGTATCCCCAAAAATAAAAAAATTAGTGTTTTGGAAGTAAAAAAAGGGTTGGAGTATCCCCTCA
1 GAGTATCCCCGAAGAT-AAAAATTTGGTGTTTTGGAAGTAAAAAAGGGGTTGGAGTATCCCCTCA
* * * * *
28425 GAGATGGTGCGATTAGAGTATCCCCGAAGATGACAATTTGATATTTTCATAAATT-AAACTTTAG
65 GAGATGGTGGGGTTGGAGTAT-CCTGAAGATGACAATTT--CATTTTCATAAATTGAAA-TTTAG
* * * * *
28489 TCTTAAAATAGGGTTGGAGTAT-CTCCTCGGAGAT-AGTAGGGTTA
126 TGTAAAAACAGGGTT-GAGTATCCT-CTCAGAGATGA-TGGGGTTA
* ** *
28533 GAGTATCCCTGAAGAT-AAAATTTGGCATTTTGGAAGTAAAAATGGGGTTGGAGTATCCCCT
1 GAGTATCCCCGAAGATAAAAATTTGGTGTTTTGGAAGTAAAAAAGGGGTTGGAGTATCCCCT
28594 TTTAATGTTT
Statistics
Matches: 335, Mismatches: 60, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
170 3 0.01
171 96 0.29
172 69 0.21
173 161 0.48
174 4 0.01
175 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (168 bp):
GAGTATCCCCGAAGATAAAAATTTGGTGTTTTGGAAGTAAAAAAGGGGTTGGAGTATCCCCTCAG
AGATGGTGGGGTTGGAGTATCCTGAAGATGACAATTTCATTTTCATAAATTGAAATTTAGTGTAA
AAACAGGGTTGAGTATCCTCTCAGAGATGATGGGGTTA
Found at i:29971 original size:20 final size:20
Alignment explanation
Indices: 29925--29976 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
29915 TACAATTCTT
* *
29925 TATGTATCGATACTATGAAC
1 TATGTATCGATACAAAGAAC
29945 T-TGTATCGATACAAAGTAA-
1 TATGTATCGATACAAAG-AAC
29964 TATGTATCGATAC
1 TATGTATCGATAC
29977 TTCTGGGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
TATGTATCGATACAAAGAAC
Found at i:30731 original size:23 final size:23
Alignment explanation
Indices: 30705--30772 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
30695 TCAAAGGAAA
30705 TTTATTGCATTCAATGACATGCT
1 TTTATTGCATTCAATGACATGCT
* * *
30728 TTTATT--AATC-A--ACAAG-A
1 TTTATTGCATTCAATGACATGCT
*
30745 TATATTGCATTCAATGACATGCT
1 TTTATTGCATTCAATGACATGCT
30768 TTTAT
1 TTTAT
30773 CAATCAACAA
Statistics
Matches: 31, Mismatches: 8, Indels: 12
0.61 0.16 0.24
Matches are distributed among these distances:
17 5 0.16
18 4 0.13
19 3 0.10
20 2 0.06
21 3 0.10
22 4 0.13
23 10 0.32
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (23 bp):
TTTATTGCATTCAATGACATGCT
Found at i:30751 original size:40 final size:40
Alignment explanation
Indices: 30707--30795 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
30697 AAAGGAAATT
* *
30707 TATTGCATTCAATGACATGCTTTTATTAATCAACAAGATA
1 TATTGCATTCAATGACATGCTTTTATCAATCAACAAGACA
30747 TATTGCATTCAATGACATGCTTTTATCAATCAACAAGACA
1 TATTGCATTCAATGACATGCTTTTATCAATCAACAAGACA
30787 TATTGCATT
1 TATTGCATT
30796 TATGTAGACA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (40 bp):
TATTGCATTCAATGACATGCTTTTATCAATCAACAAGACA
Found at i:34482 original size:20 final size:20
Alignment explanation
Indices: 34457--34514 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
34447 CTGCTAGTTT
*
34457 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
34477 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
34496 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
34515 TCGATACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:34516 original size:13 final size:13
Alignment explanation
Indices: 34498--34522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34488 ACAATGAACA
34498 TGTATCGATACAT
1 TGTATCGATACAT
34511 TGTATCGATACA
1 TGTATCGATACA
34523 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:36882 original size:20 final size:21
Alignment explanation
Indices: 36857--36896 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
36847 TTTGTTGGTG
*
36857 ATTTTGATG-AAAAATGAAGT
1 ATTTTGAAGTAAAAATGAAGT
36877 ATTTTGAAGTAAAAATGAAG
1 ATTTTGAAGTAAAAATGAAG
36897 AAATTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (21 bp):
ATTTTGAAGTAAAAATGAAGT
Found at i:43256 original size:33 final size:33
Alignment explanation
Indices: 43193--43261 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
43183 CCGTTAGAAG
* * *
43193 CAATGTATCGATACAATTCATCGTGCATCGATA
1 CAATGTATCAATACAATTCACCATGCATCGATA
*
43226 CAATGTATCAATACAATGT-ACCATGTATCGATA
1 CAATGTATCAATACAAT-TCACCATGCATCGATA
43259 CAA
1 CAA
43262 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (33 bp):
CAATGTATCAATACAATTCACCATGCATCGATA
Found at i:43315 original size:20 final size:20
Alignment explanation
Indices: 43290--43347 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
43280 CTACTAGTTT
* *
43290 CATGTATTGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
43310 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
43329 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
43348 TCAATACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.55
20 14 0.42
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:49035 original size:13 final size:13
Alignment explanation
Indices: 49017--49041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49007 CAAAGATCAG
49017 TGTATCGATACAA
1 TGTATCGATACAA
49030 TGTATCGATACA
1 TGTATCGATACA
49042 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:49130 original size:32 final size:32
Alignment explanation
Indices: 49089--49156 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
49079 TTCGTAACTG
*
49089 TACATTGTATCGATACAAAATTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
* *
49121 TACATTGTATCGATACAACACTTATGTATCTA
1 TACATTGTATCGATACAAAACTTATGTATCGA
49153 TACA
1 TACA
49157 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:49131 original size:13 final size:13
Alignment explanation
Indices: 49113--49137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49103 ACAAAATTTA
49113 TGTATCGATACAT
1 TGTATCGATACAT
49126 TGTATCGATACA
1 TGTATCGATACA
49138 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:49150 original size:19 final size:18
Alignment explanation
Indices: 49094--49157 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
49084 AACTGTACAT
*
49094 TGTATCGATACAAAATTTA
1 TGTATCGATACAACA-TTA
49113 TGTATCGAT---ACA-T-
1 TGTATCGATACAACATTA
49126 TGTATCGATACAACACTTA
1 TGTATCGATACAACA-TTA
*
49145 TGTATCTATACAA
1 TGTATCGATACAA
49158 ATCGTTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 5 0.14
18 1 0.03
19 21 0.57
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (18 bp):
TGTATCGATACAACATTA
Found at i:49220 original size:21 final size:22
Alignment explanation
Indices: 49194--49236 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
49184 GTTGGGACCT
*
49194 TGTATCGATACATTT-GACAAA
1 TGTATCAATACATTTGGACAAA
49215 TGTATCAATACATTTGGACAAA
1 TGTATCAATACATTTGGACAAA
49237 AATGTGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (22 bp):
TGTATCAATACATTTGGACAAA
Found at i:49972 original size:49 final size:48
Alignment explanation
Indices: 49903--50467 Score: 705
Period size: 49 Copynumber: 11.9 Consensus size: 48
49893 AAGATGGAAA
* * * *
49903 AGGTGCCAATATGCTAATTCAAGGCCAGCGATATCGGACTTAAAGGTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* * *
49951 AAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 -AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
*
50000 AGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTT--A-A--
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* *
50043 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-T-AAGATG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
*
50089 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
*
50137 AGGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTT--A-A--
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* ** * *
50180 AGGTACCAATGCGCTGATTCAAGGCTAGCTACATTGGACTTAAAGATG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
50228 AGGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-A--
1 A-GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* * *
50272 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATG
1 AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
50320 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
1 -AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
* * *
50369 AGGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGATG
1 A-GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AAAGATG
* *
50419 ACAACGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 ---A-GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
50468 GAAGATGCCA
Statistics
Matches: 453, Mismatches: 40, Indels: 43
0.85 0.07 0.08
Matches are distributed among these distances:
42 1 0.00
43 112 0.25
44 2 0.00
45 3 0.01
46 42 0.09
47 2 0.00
48 84 0.19
49 158 0.35
50 7 0.02
52 4 0.01
53 38 0.08
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (48 bp):
AGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
Found at i:50271 original size:92 final size:91
Alignment explanation
Indices: 49901--50468 Score: 669
Period size: 92 Copynumber: 6.1 Consensus size: 91
49891 TCAAGATGGA
* * * * * * *
49901 AAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATCGGACTTAAAGGTGAAGATGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGCCAATATGC
*
49966 TGATTCAAGGCCAGCTACATTGGACTT
65 TGATTCAAGGCCAGCTATATTGGACTT
* *
49993 AAAGATGAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTT--A-A--AGGTGCCAAT
1 --A-A--AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGGTGCCAAT
* * *
50053 GTGCTGATTCAAGGCCAGCTACATTGGACTA
61 ATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
50084 AGATGAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAGGTGCCAATAT
1 A-A--AGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGGTGCCAATAT
*
50149 GCTGATTCAAGGCTAGCTATATTGGACTT
63 GCTGATTCAAGGCCAGCTATATTGGACTT
* ** *
50178 AAAGGTACCAATGCGCTGATTCAAGGCTAGCTACATTGGACTTAAAGATGAGGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA-GGTGCCAATATGC
50243 TGATTCAAGGCCAGCTATATTGGACTT
65 TGATTCAAGGCCAGCTATATTGGACTT
* *
50270 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATGAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGCCAATATGC
50335 TGATTCAAGGCCAGCTATATTGGACTT
65 TGATTCAAGGCCAGCTATATTGGACTT
* * *
50362 AAAGATGAGGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGATGACAACGGC
1 --A-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGATG---A-GGT
*
50427 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
55 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
50464 AAAGG
1 AAAGG
50469 AAGATGCCAC
Statistics
Matches: 428, Mismatches: 26, Indels: 38
0.87 0.05 0.08
Matches are distributed among these distances:
89 45 0.11
91 83 0.19
92 125 0.29
93 2 0.00
94 40 0.09
95 3 0.01
96 2 0.00
97 41 0.10
98 39 0.09
99 7 0.02
100 1 0.00
101 2 0.00
102 38 0.09
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (91 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGGTGCCAATATGCT
GATTCAAGGCCAGCTATATTGGACTT
Found at i:50556 original size:34 final size:34
Alignment explanation
Indices: 50509--50639 Score: 244
Period size: 34 Copynumber: 3.9 Consensus size: 34
50499 AAAGGAGAAA
50509 GATGCCACGGAGTTGTGGACTTAAAAGGAACAAG
1 GATGCCACGGAGTTGTGGACTTAAAAGGAACAAG
*
50543 GATGCCACAGAGTTGTGGACTTAAAAGGAACAAG
1 GATGCCACGGAGTTGTGGACTTAAAAGGAACAAG
50577 GATGCCACGGAGTTGTGGACTTAAAAGGAACAAG
1 GATGCCACGGAGTTGTGGACTTAAAAGGAACAAG
*
50611 GATGCCCCGGAGTTGTGGACTTAAAAGGA
1 GATGCCACGGAGTTGTGGACTTAAAAGGA
50640 TGCCACGGAG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 94 1.00
ACGTcount: A:0.34, C:0.15, G:0.32, T:0.18
Consensus pattern (34 bp):
GATGCCACGGAGTTGTGGACTTAAAAGGAACAAG
Found at i:50648 original size:27 final size:29
Alignment explanation
Indices: 50611--50752 Score: 135
Period size: 31 Copynumber: 4.8 Consensus size: 29
50601 AAGGAACAAG
* *
50611 GATGCCCCGGAGTTGTGGAC-TTAAAAG-
1 GATGCCACGGAGTCGTGGACTTTAAAAGA
* *
50638 GATGCCACGGAGTTGTGGGCTTTAGAAAGA
1 GATGCCACGGAGTCGTGGACTTTA-AAAGA
* *
50668 GATTGCCACTGAGTCGTGGACTTTGGAAAGA
1 GA-TGCCACGGAGTCGTGGACTTT-AAAAGA
* *
50699 GATGCCACTGAGTCGTGGACTTTGAAGAAAA
1 GATGCCACGGAGTCGTGGACTTT-AA-AAGA
* *
50730 AATGCCACTGAGTCGTGGACTTT
1 GATGCCACGGAGTCGTGGACTTT
50753 GGGACAAAAT
Statistics
Matches: 100, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
27 18 0.18
28 3 0.03
29 4 0.04
30 25 0.25
31 50 0.50
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.25
Consensus pattern (29 bp):
GATGCCACGGAGTCGTGGACTTTAAAAGA
Found at i:50703 original size:61 final size:60
Alignment explanation
Indices: 50634--50787 Score: 192
Period size: 61 Copynumber: 2.6 Consensus size: 60
50624 TGTGGACTTA
* * *
50634 AAAG-GATGCCACGGAGTTGTGGGCTTTAGAAAGAGATTGCCACTGAGTCGTGGACTTT-GG
1 AAAGAGATGCCACTGAGTCGTGGGCTTTAGAAA-A-AATGCCACTGAGTCGTGGACTTTGGG
*
50694 AAAGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGGG
1 AAAGAGATGCCACTGAGTCGTGGGCTTT--AGAAAAAATGCCACTGAGTCGTGGACTTTGGG
50756 ACAA-A-ATGCCACTGAGTCGTGGGCTTT-GAAAA
1 A-AAGAGATGCCACTGAGTCGTGGGCTTTAGAAAA
50788 GGTATTTGAA
Statistics
Matches: 84, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
58 5 0.06
60 4 0.05
61 63 0.75
62 5 0.06
63 7 0.08
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.23
Consensus pattern (60 bp):
AAAGAGATGCCACTGAGTCGTGGGCTTTAGAAAAAATGCCACTGAGTCGTGGACTTTGGG
Found at i:50707 original size:30 final size:30
Alignment explanation
Indices: 50634--50788 Score: 174
Period size: 31 Copynumber: 5.1 Consensus size: 30
50624 TGTGGACTTA
* * * *
50634 AAAG-GATGCCACGGAGTTGTGGGCTTTAG
1 AAAGAGATGCCACTGAGTCGTGGACTTTGG
50663 AAAGAGATTGCCACTGAGTCGTGGACTTTGG
1 AAAGAGA-TGCCACTGAGTCGTGGACTTTGG
50694 AAAGAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAGAGATGCCACTGAGTCGTGGACTTTG--G
*
50726 AAA-AAATGCCACTGAGTCGTGGACTTTGGG
1 AAAGAGATGCCACTGAGTCGTGGACTTT-GG
* *
50756 ACAA-A-ATGCCACTGAGTCGTGGGCTTTGA
1 A-AAGAGATGCCACTGAGTCGTGGACTTTGG
50785 AAAG
1 AAAG
50789 GTATTTGAAG
Statistics
Matches: 112, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.02
29 6 0.05
30 47 0.42
31 52 0.46
32 5 0.04
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (30 bp):
AAAGAGATGCCACTGAGTCGTGGACTTTGG
Found at i:52025 original size:13 final size:13
Alignment explanation
Indices: 52007--52044 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
51997 GCCTTTGCAC
52007 TTTTTTTTGTGTG
1 TTTTTTTTGTGTG
*
52020 -TTTTTTTGTTTTG
1 TTTTTTTTG-TGTG
52033 TTTTTTTTGTGT
1 TTTTTTTTGTGT
52045 TTACTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 8 0.38
13 5 0.24
14 8 0.38
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (13 bp):
TTTTTTTTGTGTG
Found at i:57236 original size:20 final size:21
Alignment explanation
Indices: 57197--57236 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
57187 AAAACAACAT
*
57197 AATTGAACACCAACTATCAAC
1 AATTAAACACCAACTATCAAC
*
57218 AATTAAACA-CAATTATCAA
1 AATTAAACACCAACTATCAA
57237 AAATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.53, C:0.23, G:0.03, T:0.23
Consensus pattern (21 bp):
AATTAAACACCAACTATCAAC
Found at i:62434 original size:15 final size:15
Alignment explanation
Indices: 62414--62444 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
62404 TAAAAATGTC
*
62414 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
62429 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
62444 C
1 C
62445 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:64533 original size:13 final size:13
Alignment explanation
Indices: 64515--64553 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
64505 ACATTTTTCC
64515 TTGTATCGATACA
1 TTGTATCGATACA
64528 TTGTATCGATACA
1 TTGTATCGATACA
*
64541 CTGTATCGATACA
1 TTGTATCGATACA
64554 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:66379 original size:37 final size:34
Alignment explanation
Indices: 66346--66444 Score: 157
Period size: 37 Copynumber: 2.9 Consensus size: 34
66336 AATTTTGATA
66346 TGAATTACTTGATTAAGGGGGAGA--TTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTT
66378 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGA---TTTTTTTTTT
66415 TGAATTACTTGATTAAGGGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
66445 AATAAACGGG
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
32 24 0.39
34 6 0.10
37 32 0.52
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.48
Consensus pattern (34 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTTTTT
Found at i:67088 original size:20 final size:20
Alignment explanation
Indices: 67065--67137 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
67055 ACAATTCAAA
67065 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
67085 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
67106 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
67126 GTATCGATACAT
1 GTATCGATACAT
67138 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:67108 original size:21 final size:21
Alignment explanation
Indices: 67082--67158 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
67072 TACATGTTGC
67082 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
67103 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
67123 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
67143 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
67159 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:67116 original size:41 final size:41
Alignment explanation
Indices: 67065--67158 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
67055 ACAATTCAAA
67065 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
67106 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
67147 GTATCGATACAT
1 GTATCGATACAT
67159 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:67215 original size:13 final size:13
Alignment explanation
Indices: 67197--67222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67187 TACAGCAAGT
67197 ATGTATCGATACA
1 ATGTATCGATACA
67210 ATGTATCGATACA
1 ATGTATCGATACA
67223 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:69266 original size:21 final size:21
Alignment explanation
Indices: 69226--69266 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
69216 TTAAGTATAA
*
69226 ATATTTTTCAAGCTATAAATC
1 ATATTTTTCAAGCTAAAAATC
69247 ATATGTTTTCAAG-TAAAAAT
1 ATAT-TTTTCAAGCTAAAAAT
69267 AATCCAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (21 bp):
ATATTTTTCAAGCTAAAAATC
Found at i:71113 original size:9 final size:9
Alignment explanation
Indices: 71096--71134 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
71086 TCAACCATCA
71096 AAGATGATG
1 AAGATGATG
*
71105 AAAATGATG
1 AAGATGATG
*
71114 ATGATGATG
1 AAGATGATG
*
71123 ATGATGATG
1 AAGATGATG
71132 AAG
1 AAG
71135 TTGACTCGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.26
Consensus pattern (9 bp):
AAGATGATG
Found at i:71114 original size:3 final size:3
Alignment explanation
Indices: 71098--71132 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
71088 AACCATCAAA
* *
71098 GAT GAT GAA AAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
71133 AGTTGACTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (3 bp):
GAT
Done.