Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1431
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: 237145
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
File 2 of 2
Found at i:182643 original size:42 final size:42
Alignment explanation
Indices: 182595--182675 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
182585 CTTCTTCTCT
* * *
182595 TCTCCTCCTATCATCCCTTCTCTCTCTATTATCTCTCCTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
*
182637 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTTTCCT
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCT
182676 CCAATCATCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.12, C:0.43, G:0.00, T:0.44
Consensus pattern (42 bp):
TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
Found at i:182644 original size:12 final size:12
Alignment explanation
Indices: 182629--182663 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
182619 TCTATTATCT
182629 CTCCTATCTCTC
1 CTCCTATCTCTC
182641 CTCCTATCATC-C
1 CTCCTATC-TCTC
182653 CTCCTATCTCT
1 CTCCTATCTCT
182664 ACTATCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:182647 original size:24 final size:22
Alignment explanation
Indices: 182613--182663 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
182603 TATCATCCCT
* *
182613 TCTCTCTCTATTATCTCTCCTA
1 TCTCTCTCTATCATCCCTCCTA
182635 TCTCTCCTCCTATCATCCCTCCTA
1 TCTCT-CT-CTATCATCCCTCCTA
182659 TCTCT
1 TCTCT
182664 ACTATCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.20
23 2 0.08
24 18 0.72
ACGTcount: A:0.12, C:0.43, G:0.00, T:0.45
Consensus pattern (22 bp):
TCTCTCTCTATCATCCCTCCTA
Found at i:182661 original size:33 final size:33
Alignment explanation
Indices: 182624--182694 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
182614 CTCTCTCTAT
* *
182624 TATCTCTCCTATCTCTCCTCCTATCATCCCTCC
1 TATCTCTACTATCTCTCCTCCAATCATCCCTCC
*
182657 TATCTCTACTATCTTTCCTCCAATCATCCCTCC
1 TATCTCTACTATCTCTCCTCCAATCATCCCTCC
182690 TATCT
1 TATCT
182695 TTTCTTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.15, C:0.44, G:0.00, T:0.41
Consensus pattern (33 bp):
TATCTCTACTATCTCTCCTCCAATCATCCCTCC
Found at i:184611 original size:9 final size:9
Alignment explanation
Indices: 184597--184657 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 9
184587 GGATGATAGG
*
184597 AGGAGATAT
1 AGGAGAGAT
184606 AGGAGAGAT
1 AGGAGAGAT
*
184615 AGTAGAGAT
1 AGGAGAGAT
184624 AGGAGGGATGATT
1 AGGA--GA-GA-T
184637 GCAGGAGAGAT
1 --AGGAGAGAT
184648 AGGAGAGAT
1 AGGAGAGAT
184657 A
1 A
184658 ATAGAGAGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
9 29 0.67
11 3 0.07
12 4 0.09
13 3 0.07
15 4 0.09
ACGTcount: A:0.41, C:0.02, G:0.41, T:0.16
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:184627 original size:42 final size:42
Alignment explanation
Indices: 184580--184686 Score: 160
Period size: 42 Copynumber: 2.5 Consensus size: 42
184570 GAAAGAAGAA
* *
184580 ATAGGAGGGATGATAGGAGGAGATATAGGAGAGATAGTAGAG
1 ATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAG
* *
184622 ATAGGAGGGATGATTGCAGGAGAGATAGGAGAGATAATAGAG
1 ATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAG
* *
184664 AGAGGAGGGATGACAGGAGGAGA
1 ATAGGAGGGATGATAGGAGGAGA
184687 AGAGAAGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.40, C:0.02, G:0.44, T:0.14
Consensus pattern (42 bp):
ATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAATAGAG
Found at i:190011 original size:9 final size:9
Alignment explanation
Indices: 189997--190045 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
189987 TGATAGGAGC
189997 AGAGATAGG
1 AGAGATAGG
*
190006 AGAGATAGT
1 AGAGATAGG
190015 AGAGATAGG
1 AGAGATAGG
*
190024 AGGGAT--G
1 AGAGATAGG
*
190031 ATAGA-AGG
1 AGAGATAGG
190039 AGAGATA
1 AGAGATA
190046 ATGGAGAGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
7 4 0.13
8 5 0.16
9 22 0.71
ACGTcount: A:0.45, C:0.00, G:0.41, T:0.14
Consensus pattern (9 bp):
AGAGATAGG
Found at i:190020 original size:18 final size:17
Alignment explanation
Indices: 189997--190045 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
189987 TGATAGGAGC
189997 AGAGATAGGAGAGATAG
1 AGAGATAGGAGAGATAG
*
190014 TAGAGATAGGAGGGAT-G
1 -AGAGATAGGAGAGATAG
*
190031 ATAGA-AGGAGAGATA
1 AGAGATAGGAGAGATA
190046 ATGGAGAGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.30
16 4 0.15
17 1 0.04
18 14 0.52
ACGTcount: A:0.45, C:0.00, G:0.41, T:0.14
Consensus pattern (17 bp):
AGAGATAGGAGAGATAG
Found at i:190027 original size:42 final size:44
Alignment explanation
Indices: 189964--190054 Score: 123
Period size: 42 Copynumber: 2.1 Consensus size: 44
189954 TAGCCCATAA
*
189964 AGAGAAAGAAGAGATAAGAGGGATGATAGGAGCAGAGAT-A-GG
1 AGAGAAAGAAGAGATAAGAGGGATGATAGAAGCAGAGATAATGG
* * * *
190006 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAATGG
1 AGAGAAAGAAGAGATAAGAGGGATGATAGAAGCAGAGATAATGG
190050 AGAGA
1 AGAGA
190055 GGAGGTATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 34 0.81
43 1 0.02
44 7 0.17
ACGTcount: A:0.46, C:0.01, G:0.41, T:0.12
Consensus pattern (44 bp):
AGAGAAAGAAGAGATAAGAGGGATGATAGAAGCAGAGATAATGG
Found at i:190040 original size:33 final size:33
Alignment explanation
Indices: 190003--190077 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
189993 GAGCAGAGAT
* *
190003 AGGAGAGATAGTAGAGATAGGAGGGATGATAGA
1 AGGAGAGATAATAGAGAGAGGAGGGATGATAGA
* * *
190036 AGGAGAGATAATGGAGAGAGGAGGTATGATAGG
1 AGGAGAGATAATAGAGAGAGGAGGGATGATAGA
190069 AGGAAGAGA
1 AGG-AGAGA
190078 GAAGAAGATG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 31 0.86
34 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.44, T:0.13
Consensus pattern (33 bp):
AGGAGAGATAATAGAGAGAGGAGGGATGATAGA
Found at i:194413 original size:262 final size:262
Alignment explanation
Indices: 193943--194461 Score: 871
Period size: 262 Copynumber: 2.0 Consensus size: 262
193933 TATAGGAAAG
* * *
193943 TTGATGAGAACCAAGGAAGGTCCATTGAAGACAACGACCTGAAGGCCTTGGGAAGGTTTCAAGGA
1 TTGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCAGAAGGCCTTGGGAAGGTTTCAAGGA
* *
194008 CCAATGACGAGGGCAAAGGCAAAGAGGACAAAGGAAGGCCTAGAGAAGATGGTTGCTGCCTTATT
66 CCAATAACGAGGGCAAAGGCAAAGAGGACAAAGGAAGACCTAGAGAAGATGGTTGCTGCCTTATT
* *
194073 TAAAAGTAGACCCAATCTGGAGTTAGAAGAGCCCAAGCTGGTCAATTGCATATATTTGGAAGATA
131 TAAAAGTAGACCCAATCTGGACTTAGAAGAGCCCAAGCTAGTCAATTGCATATATTTGGAAGATA
194138 TGGGCTCCAATGGATTGAATTAGGACTTGGGTTAATTTGTAATAAAGGGCCTGCTGGTTGTGGCT
196 TGGGCTCCAATGGATTGAATTAGGACTTGGGTTAATTTGTAATAAAGGGCCTGCTGGTTGTGGCT
194203 TA
261 TA
**
194205 TTGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCAGAAGGTGTT-GGAAGGATTTCAAGG
1 TTGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCAGAAGGCCTTGGGAAGG-TTTCAAGG
*
194269 ACCAATAACGAGGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGATGGTTGCTGGCC-TA
65 ACCAATAACGAGGGCAAAGGCAAAGAGGACAAAGGAAGACCTAGAGAAGATGGTTGCT-GCCTTA
* * *
194333 TTTGAAAGTAGACCCAATTTGGACTTAGAAGAGCCCAAGCTAGTTAATTGCATATATTTGGAAGA
129 TTTAAAAGTAGACCCAATCTGGACTTAGAAGAGCCCAAGCTAGTCAATTGCATATATTTGGAAGA
* *
194398 TATGGGCTTCAATGGATTGAATTAGGACTTGGGTTATTTTGTAATAAAGGGCCTGCTGGTTGTG
194 TATGGGCTCCAATGGATTGAATTAGGACTTGGGTTAATTTGTAATAAAGGGCCTGCTGGTTGTG
194462 ACTTGCTTTG
Statistics
Matches: 240, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
261 6 0.03
262 231 0.96
263 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (262 bp):
TTGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCAGAAGGCCTTGGGAAGGTTTCAAGGA
CCAATAACGAGGGCAAAGGCAAAGAGGACAAAGGAAGACCTAGAGAAGATGGTTGCTGCCTTATT
TAAAAGTAGACCCAATCTGGACTTAGAAGAGCCCAAGCTAGTCAATTGCATATATTTGGAAGATA
TGGGCTCCAATGGATTGAATTAGGACTTGGGTTAATTTGTAATAAAGGGCCTGCTGGTTGTGGCT
TA
Found at i:195862 original size:24 final size:24
Alignment explanation
Indices: 195829--195914 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
195819 AAGAGAAAGA
*
195829 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
195853 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
195871 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* * *
195895 AGAGCCAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
195915 AGAGAGGAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
18 11 0.23
20 2 0.04
21 6 0.12
22 2 0.04
24 27 0.56
ACGTcount: A:0.41, C:0.03, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:195881 original size:42 final size:42
Alignment explanation
Indices: 195820--195938 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
195810 TAGCCCTTAA
* *
195820 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
195862 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGCCAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
195904 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
195939 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.42, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:200552 original size:15 final size:14
Alignment explanation
Indices: 200515--200553 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
200505 AAGAATACAA
200515 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
200529 AATACAAAAAGAAAGG
1 AA-AAAAAAAGAAA-G
200545 AAAAAAAAA
1 AAAAAAAAA
200554 ACCAGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:201323 original size:12 final size:11
Alignment explanation
Indices: 201301--201376 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
201291 AGAGAAAGAA
*
201301 GAGAGAGGAGG
1 GAGATAGGAGG
201312 GATGATAGGAGG
1 GA-GATAGGAGG
*
201324 AGAGACAGGA--
1 -GAGATAGGAGG
*
201334 GAGATAGTA--
1 GAGATAGGAGG
201343 GAGATAGGAGG
1 GAGATAGGAGG
201354 GATGATAGGAGG
1 GA-GATAGGAGG
*
201366 AGAGACAGGAG
1 -GAGATAGGAG
201377 AGATAACAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:201352 original size:42 final size:42
Alignment explanation
Indices: 201291--201409 Score: 195
Period size: 42 Copynumber: 2.8 Consensus size: 42
201281 TAGCCCTCAA
*
201291 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
201333 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
201375 AGAGATA-ACAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGA-AGAGAGAGGAGGGATGATAGGAGGAG
201410 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:209005 original size:12 final size:11
Alignment explanation
Indices: 208986--209057 Score: 62
Period size: 12 Copynumber: 6.5 Consensus size: 11
208976 AGAGAAAGAA
208986 GAGATAGGAGG
1 GAGATAGGAGG
208997 GATGATAGGAGG
1 GA-GATAGGAGG
209009 AGAGATAGGA--
1 -GAGATAGGAGG
*
209019 GAGATAGTA--
1 GAGATAGGAGG
209028 GAGATAGGAGG
1 GAGATAGGAGG
*
209039 GATGATAGAAGG
1 GA-GATAGGAGG
209051 AGAGATA
1 -GAGATA
209058 AGAGAGATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
9 16 0.31
11 4 0.08
12 28 0.54
13 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:209020 original size:9 final size:9
Alignment explanation
Indices: 209006--209066 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
208996 GGATGATAGG
209006 AGGAGAGAT
1 AGGAGAGAT
209015 AGGAGAGAT
1 AGGAGAGAT
*
209024 AGTAGAGAT
1 AGGAGAGAT
*
209033 AGGAGGGAT
1 AGGAGAGAT
*
209042 --GATAGA-
1 AGGAGAGAT
209048 AGGAGAGAT
1 AGGAGAGAT
*
209057 AAGAGAGAT
1 AGGAGAGAT
209066 A
1 A
209067 ATAGAGAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 4 0.10
8 5 0.12
9 33 0.79
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:209035 original size:42 final size:42
Alignment explanation
Indices: 208976--209088 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 42
208966 TAGCTCTCAA
* * * *
208976 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAAG
209018 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAAG
1 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAAG
* *
209060 AGAGATAATAGAGAGAGGAGGGATGATAG
1 AGAGATAGTAGAGATAGGAGGGATGATAG
209089 TGATGAAAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.12
Consensus pattern (42 bp):
AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAAG
Found at i:210760 original size:42 final size:42
Alignment explanation
Indices: 210698--210826 Score: 197
Period size: 42 Copynumber: 3.1 Consensus size: 42
210688 GTAGCCCTCA
* *
210698 AAGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAG
1 AAGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAG
*
210740 AAGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAG
1 AAGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAG
* * *
210782 GAGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG-GAGAG
1 AAGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAG
210823 AAGA
1 AAGA
210827 AGATGGAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 7 0.09
42 72 0.91
ACGTcount: A:0.45, C:0.02, G:0.45, T:0.09
Consensus pattern (42 bp):
AAGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAG
Found at i:210801 original size:18 final size:18
Alignment explanation
Indices: 210774--210823 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
210764 TGATAGGAGG
*
210774 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
210792 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
210810 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
210824 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:215818 original size:21 final size:21
Alignment explanation
Indices: 215789--215828 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
215779 GGTTGTCATC
215789 AGATAGAAGGAG-GAGAGAAGA
1 AGATAGAA-GAGTGAGAGAAGA
*
215810 AGATGGAAGAGTGAGAGAA
1 AGATAGAAGAGTGAGAGAA
215829 AATGAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.50, C:0.00, G:0.42, T:0.07
Consensus pattern (21 bp):
AGATAGAAGAGTGAGAGAAGA
Found at i:216433 original size:18 final size:18
Alignment explanation
Indices: 216410--216469 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
216400 AGAAATCCTA
216410 CTAATGCTTCTACTTCTT
1 CTAATGCTTCTACTTCTT
* *
216428 CTAATGCTTCTTTTAATTCTA
1 CTAATGCTTC---TACTTCTT
216449 CTAATGCTTCTACTTCTT
1 CTAATGCTTCTACTTCTT
216467 CTA
1 CTA
216470 CTTCTAGGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 19 0.54
21 16 0.46
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.50
Consensus pattern (18 bp):
CTAATGCTTCTACTTCTT
Found at i:216468 original size:21 final size:21
Alignment explanation
Indices: 216407--216471 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
216397 GTAAGAAATC
216407 CTACTAATGCTTCTACTTC-T
1 CTACTAATGCTTCTACTTCTT
* *
216427 -T-CTAATGCTTCT-TTTAATT
1 CTACTAATGCTTCTACTT-CTT
216446 CTACTAATGCTTCTACTTCTT
1 CTACTAATGCTTCTACTTCTT
216467 CTACT
1 CTACT
216472 TCTAGGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 2 0.06
18 11 0.31
19 2 0.06
20 1 0.03
21 18 0.50
22 2 0.06
ACGTcount: A:0.20, C:0.26, G:0.05, T:0.49
Consensus pattern (21 bp):
CTACTAATGCTTCTACTTCTT
Found at i:221534 original size:20 final size:20
Alignment explanation
Indices: 221509--221560 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
221499 TACAAGCCAA
**
221509 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
221529 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
221548 TGTATCGATACAA
1 TGTATCGATACAA
221561 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:224118 original size:13 final size:13
Alignment explanation
Indices: 224100--224138 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
224090 ATAATCCCCC
224100 TGTATCGATACAA
1 TGTATCGATACAA
* *
224113 TGTATCAATACAT
1 TGTATCGATACAA
224126 TGTATCGATACAA
1 TGTATCGATACAA
224139 AGAAAAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:230306 original size:20 final size:20
Alignment explanation
Indices: 230281--230332 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
230271 TACAAGCCAA
**
230281 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
230301 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
230320 TGTATCGATACAA
1 TGTATCGATACAA
230333 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:232752 original size:15 final size:14
Alignment explanation
Indices: 232715--232753 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
232705 CAAGAATACA
232715 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
232729 AATACAAAAAGAAAGG
1 AA-AAAAAAAGAAA-G
232745 AAAAAAAAA
1 AAAAAAAAA
232754 ACCAGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:233523 original size:12 final size:11
Alignment explanation
Indices: 233501--233576 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
233491 AGAGAAAGAA
*
233501 GAGAGAGGAGG
1 GAGATAGGAGG
233512 GATGATAGGAGG
1 GA-GATAGGAGG
*
233524 AGAGACAGGA--
1 -GAGATAGGAGG
*
233534 GAGATAGTA--
1 GAGATAGGAGG
233543 GAGATAGGAGG
1 GAGATAGGAGG
233554 GATGATAGGAGG
1 GA-GATAGGAGG
*
233566 AGAGACAGGAG
1 -GAGATAGGAG
233577 AGATAACAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:233552 original size:42 final size:42
Alignment explanation
Indices: 233491--233609 Score: 195
Period size: 42 Copynumber: 2.8 Consensus size: 42
233481 TAGCCCTCAA
*
233491 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
233533 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
233575 AGAGATA-ACAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGA-AGAGAGAGGAGGGATGATAGGAGGAG
233610 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Done.