Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3102
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: 22812
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Found at i:186 original size:19 final size:19
Alignment explanation
Indices: 158--221 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
148 TGTAATTATG
*
158 TGTTACATGGATGAATTAC
1 TGTTATATGGATGAATTAC
* *
177 TGTTATATGGATGAAGTAT
1 TGTTATATGGATGAATTAC
***
196 TGTTTATACAAATGAATTAC
1 TG-TTATATGGATGAATTAC
216 TGTTAT
1 TGTTAT
222 CAATGAATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 22 0.61
20 14 0.39
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (19 bp):
TGTTATATGGATGAATTAC
Found at i:210 original size:20 final size:19
Alignment explanation
Indices: 187--241 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 19
177 TGTTATATGG
*
187 ATGAAGTATTGTTTATACAA
1 ATGAATTATTGTTTATAC-A
*
207 ATGAATTACTG-TTAT-CA
1 ATGAATTATTGTTTATACA
224 ATGAATTATTGTTTATAC
1 ATGAATTATTGTTTATAC
242 GATTGAGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 11 0.37
18 5 0.17
19 5 0.17
20 9 0.30
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (19 bp):
ATGAATTATTGTTTATACA
Found at i:237 original size:37 final size:37
Alignment explanation
Indices: 168--241 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 37
158 TGTTACATGG
168 ATGAATTACTGTTATATGGATGAAGTATTGTTTATACAA
1 ATGAATTACTGTTATA--GATGAAGTATTGTTTATACAA
*
207 ATGAATTACTGTTATCA-ATGAATTATTGTTTATAC
1 ATGAATTACTGTTAT-AGATGAAGTATTGTTTATAC
242 GATTGAGAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
37 17 0.52
39 15 0.45
40 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (37 bp):
ATGAATTACTGTTATAGATGAAGTATTGTTTATACAA
Found at i:1438 original size:13 final size:13
Alignment explanation
Indices: 1420--1444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1410 TAATGGTATA
1420 TTGAATCCATGAT
1 TTGAATCCATGAT
1433 TTGAATCCATGA
1 TTGAATCCATGA
1445 AAATTTAGTA
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):
TTGAATCCATGAT
Found at i:3507 original size:45 final size:46
Alignment explanation
Indices: 3381--3643 Score: 352
Period size: 46 Copynumber: 5.7 Consensus size: 46
3371 TTAGGATTTT
* *
3381 ATGTGATGAATGTGAATGGTGCATATATGTGATAAGGCCTAATACCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATACCG
*
3428 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAACG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATACCG
3474 ATGTGATGAATGTG-AAGTGTATATATGTGATAA-GCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATA-CCG
*
3519 ATGTGA-GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-ACCG
* * * *** *
3565 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATACCG
* * *
3611 ACGTGATGGATGTGAAAGTGTATAAATGTGATA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATA
3644 GTCCCGAAGG
Statistics
Matches: 196, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
44 15 0.08
45 46 0.23
46 89 0.45
47 46 0.23
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (46 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATACCG
Found at i:5133 original size:40 final size:40
Alignment explanation
Indices: 5075--5468 Score: 553
Period size: 40 Copynumber: 9.9 Consensus size: 40
5065 GAGTGAAATG
*
5075 TCCGGGCTAA-ATCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTC-CGAAGAGCATTCGTGCTAGTGATGTA
*
5115 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
*
5155 TTCGGGCTAAG-TCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
* *
5194 TTC-GGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
*
5233 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
5273 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
5313 TCCGGGCTAAG-TCTCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTTC-CGAAGAGCATTCGTGCTAGTGATGTA
* *
5353 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
* *** * * * *
5393 TCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTATA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
* * * * *
5433 TCCGGGCTAGGTCCCGAAGTGCAATCATGCTAGTGA
1 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA
5469 CGTGTATTCG
Statistics
Matches: 320, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
38 7 0.02
39 62 0.19
40 247 0.77
41 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
Found at i:5185 original size:22 final size:22
Alignment explanation
Indices: 5121--5224 Score: 68
Period size: 17 Copynumber: 5.1 Consensus size: 22
5111 TGTATCCGGA
5121 CTAAGTTCCGAAGAGCATTCGTG
1 CTAAG-TCCGAAGAGCATTCGTG
* * *
5144 CT-AGT--G-A-TGTATTCGGG
1 CTAAGTCCGAAGAGCATTCGTG
5161 CTAAGTCCGAAGAGCATTCGTG
1 CTAAGTCCGAAGAGCATTCGTG
* *
5183 CT-AGT--G-A-TGTATTCG-G
1 CTAAGTCCGAAGAGCATTCGTG
5199 CTAAGTCCCGAAGAGCATTCGTG
1 CTAAGT-CCGAAGAGCATTCGTG
5222 CTA
1 CTA
5225 GTGATGTATC
Statistics
Matches: 59, Mismatches: 10, Indels: 24
0.63 0.11 0.26
Matches are distributed among these distances:
16 3 0.05
17 18 0.31
18 5 0.08
19 2 0.03
20 2 0.03
21 6 0.10
22 17 0.29
23 6 0.10
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (22 bp):
CTAAGTCCGAAGAGCATTCGTG
Found at i:5395 original size:120 final size:119
Alignment explanation
Indices: 5075--5468 Score: 610
Period size: 120 Copynumber: 3.3 Consensus size: 119
5065 GAGTGAAATG
* *
5075 TCCGGGCTAAATCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATT
*
5140 CGTGCTAGTGATGTATTCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTA
66 CGTGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTA
*
5194 TTC-GGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATT
5258 CGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
66 CGTGCTAGTGATGTATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTAGTGATGTA
*
5313 TCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATT
* * ** * * * *
5378 CGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTATA
66 CGTGCTAGTGATGTATCCGGGCT-AAGTCCGAAGAGCATTCGTGCTAGTGATGTA
* * * *
5433 TCCGGGCTAGGTCCCGAAGTGCAATCATGCTAGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
5469 CGTGTATTCG
Statistics
Matches: 253, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
118 84 0.33
119 32 0.13
120 135 0.53
121 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (119 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATT
CGTGCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTAGTGATGTA
Found at i:7665 original size:13 final size:13
Alignment explanation
Indices: 7647--7671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7637 TAATGGTATA
7647 TTGAATCCATGAT
1 TTGAATCCATGAT
7660 TTGAATCCATGA
1 TTGAATCCATGA
7672 AAATTTAGTA
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):
TTGAATCCATGAT
Found at i:9685 original size:47 final size:47
Alignment explanation
Indices: 9631--9900 Score: 423
Period size: 47 Copynumber: 5.7 Consensus size: 47
9621 TTAGGATTTT
* *
9631 ATGTGATGAATGTGAATGTGCATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
*
9678 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAACCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
9725 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
*
9772 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
* * * * * *
9819 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
* * *
9866 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
9901 TCCCGAAGGG
Statistics
Matches: 208, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 208 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
Found at i:11411 original size:40 final size:40
Alignment explanation
Indices: 11352--11748 Score: 564
Period size: 40 Copynumber: 9.9 Consensus size: 40
11342 TGAGAGTGAA
*
11352 ATCCGGGCTAA-ATCTCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTC-CGAAGAGCATTCGTGCTAGTGATGT
*
11392 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
* *
11432 ATTCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
* *
11472 ATTCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
*
11512 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
11552 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
11592 ATCCGGGCTAAG-TCTCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTC-CGAAGAGCATTCGTGCTAGTGATGT
* *
11632 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
* *** * * * *
11672 ATCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
* * * * *
11712 ATCCGGGCTAGGTCCCGAAGTGCAATCATGCTAGTGA
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA
11749 CGTGTATTCG
Statistics
Matches: 325, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 319 0.98
41 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
Found at i:11464 original size:23 final size:23
Alignment explanation
Indices: 11432--11504 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
11422 CTAGTGATGT
11432 ATTCGGGCTAAGTCCCGAAGAGC
1 ATTCGGGCTAAGTCCCGAAGAGC
* * *
11455 ATTCGTGCT-AGT---G-A-TGT
1 ATTCGGGCTAAGTCCCGAAGAGC
11472 ATTCGGGCTAAGTCCCGAAGAGC
1 ATTCGGGCTAAGTCCCGAAGAGC
*
11495 ATTCGTGCTA
1 ATTCGGGCTA
11505 GTGATGTATC
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
17 9 0.24
18 4 0.11
19 1 0.03
21 1 0.03
22 4 0.11
23 18 0.49
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (23 bp):
ATTCGGGCTAAGTCCCGAAGAGC
Found at i:11522 original size:120 final size:120
Alignment explanation
Indices: 11352--11748 Score: 632
Period size: 120 Copynumber: 3.3 Consensus size: 120
11342 TGAGAGTGAA
* *
11352 ATCCGGGCTAAATCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
*
11417 TCGTGCTAGTGATGTATTCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
66 TCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
*
11472 ATTCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
*
11537 TCGTGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
66 TCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
*
11592 ATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
* * ** * * * *
11657 TCGTGCTAGTGATATATCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTAT
66 TCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
* * * *
11712 ATCCGGGCTAGGTCCCGAAGTGCAATCATGCTAGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
11749 CGTGTATTCG
Statistics
Matches: 256, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 256 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
TCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
Found at i:13949 original size:13 final size:13
Alignment explanation
Indices: 13931--13955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13921 TAATGGTATA
13931 TTGAATCCATGAT
1 TTGAATCCATGAT
13944 TTGAATCCATGA
1 TTGAATCCATGA
13956 AAATTTAGTA
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):
TTGAATCCATGAT
Found at i:15973 original size:47 final size:47
Alignment explanation
Indices: 15919--16141 Score: 329
Period size: 47 Copynumber: 4.7 Consensus size: 47
15909 TTAGGATTTT
* *
15919 ATGTGATGAATGTGAATGTGCATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
*
15966 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAACCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
*
16013 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
* * * * * *
16060 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
* * *
16107 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
16142 TCCCGAAGGG
Statistics
Matches: 161, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 161 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
Found at i:20324 original size:46 final size:45
Alignment explanation
Indices: 20203--20414 Score: 179
Period size: 46 Copynumber: 4.7 Consensus size: 45
20193 GGGTTATCGT
* *** *
20203 GAGCTAGTGTAAGA-CATGTCTGGGACATCCATCGGCCACATTATGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCTTGA-GAT-A
* *
20249 GAGCT-GATGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACAA
1 GAGCTAG-TGTAAGACCATGTCTGGGACAT-GCATCGGC-TTGAGA-TA
** *
20297 GAGCTAGT-TAAGA-CATGTCTGGGACATGCATCAACCTCGAGAT-
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATC-GGCTTGAGATA
20340 GTAAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCTATGAGATA
1 G--AGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCT-TGAGATA
*
20387 G-TC-AGTGTAAGACCATGTCTGGGACATG
1 GAGCTAGTGTAAGACCATGTCTGGGACATG
20415 GCATTGACTT
Statistics
Matches: 137, Mismatches: 16, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
43 10 0.07
44 16 0.12
45 20 0.15
46 55 0.40
47 19 0.14
48 15 0.11
49 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (45 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCTTGAGATA
Found at i:21938 original size:10 final size:10
Alignment explanation
Indices: 21918--21990 Score: 78
Period size: 10 Copynumber: 7.2 Consensus size: 10
21908 TCTCAACAAA
21918 AATTACAAAAT
1 AATT-CAAAAT
21929 AATTCAAAAT
1 AATTCAAAAT
*
21939 AATTTCCAAA-
1 AA-TTCAAAAT
21949 AATTCAAAAT
1 AATTCAAAAT
21959 AATTCAAAAT
1 AATTCAAAAT
*
21969 AATTTCCAAA-
1 AA-TTCAAAAT
*
21979 GATTCAAAAT
1 AATTCAAAAT
21989 AA
1 AA
21991 ATTTTAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
9 12 0.23
10 24 0.46
11 16 0.31
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (10 bp):
AATTCAAAAT
Found at i:21954 original size:20 final size:20
Alignment explanation
Indices: 21915--22024 Score: 81
Period size: 19 Copynumber: 5.5 Consensus size: 20
21905 CTCTCTCAAC
21915 AAAAATTACAAAATAA-TTCA
1 AAAAATT-CAAAATAATTTCA
*
21935 AAATAATTTCCAAA-AA-TTCA
1 AAA-AA-TTCAAAATAATTTCA
*
21955 AAATAATTCAAAATAATTTCC
1 AAA-AATTCAAAATAATTTCA
*
21976 AAAGATTCAAAATAAATTT--
1 AAAAATTCAAAAT-AATTTCA
*
21995 TAAAATTCAAAAT-ATTT-A
1 AAAAATTCAAAATAATTTCA
22013 TAAAAATTCAAA
1 -AAAAATTCAAA
22025 TTTTATATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
17 4 0.05
19 27 0.36
20 26 0.34
21 17 0.22
22 2 0.03
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.31
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTCA
Found at i:21959 original size:30 final size:30
Alignment explanation
Indices: 21914--21990 Score: 136
Period size: 30 Copynumber: 2.5 Consensus size: 30
21904 TCTCTCTCAA
21914 CAAAAATTACAAAATAATTCAAAATAATTTC
1 CAAAAATT-CAAAATAATTCAAAATAATTTC
21945 CAAAAATTCAAAATAATTCAAAATAATTTC
1 CAAAAATTCAAAATAATTCAAAATAATTTC
*
21975 CAAAGATTCAAAATAA
1 CAAAAATTCAAAATAA
21991 ATTTTAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 37 0.82
31 8 0.18
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.27
Consensus pattern (30 bp):
CAAAAATTCAAAATAATTCAAAATAATTTC
Found at i:22004 original size:19 final size:20
Alignment explanation
Indices: 21959--22008 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
21949 AATTCAAAAT
21959 AATTCAAAAT-AATTTCCAA
1 AATTCAAAATAAATTTCCAA
*
21978 AGATTCAAAATAAATTT-TAA
1 A-ATTCAAAATAAATTTCCAA
21998 AATTCAAAATA
1 AATTCAAAATA
22009 TTTATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.39
20 12 0.43
21 5 0.18
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (20 bp):
AATTCAAAATAAATTTCCAA
Done.