Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1652
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: 199341
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
File 4 of 4
Found at i:135733 original size:13 final size:13
Alignment explanation
Indices: 135715--135739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
135705 CAAAGATCAG
135715 TGTATCGATACAA
1 TGTATCGATACAA
135728 TGTATCGATACA
1 TGTATCGATACA
135740 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:135817 original size:33 final size:33
Alignment explanation
Indices: 135780--135846 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
135770 AGTAGCTTAA
135780 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
135813 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
135846 A
1 A
135847 AATCGTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:135820 original size:13 final size:13
Alignment explanation
Indices: 135802--135826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
135792 CAAAAAAATA
135802 TGTATCGATACAT
1 TGTATCGATACAT
135815 TGTATCGATACA
1 TGTATCGATACA
135827 ACATTTTATG
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:153353 original size:23 final size:19
Alignment explanation
Indices: 153307--153375 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 19
153297 ACATTTGTTA
153307 GGTATACATTATTTATTAG
1 GGTATACATTATTTATTAG
153326 GGTATACATTATTTATTAAG
1 GGTATACATTATTTATT-AG
* * *
153346 ATATGTATGCATTATTTTTTAG
1 ---GGTATACATTATTTATTAG
153368 GGTATACA
1 GGTATACA
153376 AGTGGAAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 23 0.56
20 2 0.05
22 2 0.05
23 14 0.34
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (19 bp):
GGTATACATTATTTATTAG
Found at i:154122 original size:39 final size:39
Alignment explanation
Indices: 154063--154145 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
154053 TTATATTAGG
* *
154063 AAATATTTGTCATGCTGCATTTGTAAAGAGAACTTTTGA
1 AAATCTTTGTCATGCTGCATTTGTAAAGAGAACTCTTGA
*
154102 AAATCTTTGTCATGCTGCATTTGTAAGGAGAACTCTTGA
1 AAATCTTTGTCATGCTGCATTTGTAAAGAGAACTCTTGA
154141 AAATC
1 AAATC
154146 CTATATTCGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (39 bp):
AAATCTTTGTCATGCTGCATTTGTAAAGAGAACTCTTGA
Found at i:155108 original size:2 final size:2
Alignment explanation
Indices: 155101--155134 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
155091 GGATATAAAC
155101 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155135 TATCTTAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:167862 original size:13 final size:13
Alignment explanation
Indices: 167844--167873 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
167834 CAATTCATCA
167844 TGTATCGATACAG
1 TGTATCGATACAG
*
167857 TGTATCGATACAT
1 TGTATCGATACAG
167870 TGTA
1 TGTA
167874 CCATGTATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:167866 original size:33 final size:33
Alignment explanation
Indices: 167824--167888 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
167814 TTGGAAGCAA
*
167824 TGTATCGATACAATT-CATCATGTATCGATACAG
1 TGTATCGATAC-ATTGCACCATGTATCGATACAG
*
167857 TGTATCGATACATTGTACCATGTATCGATACA
1 TGTATCGATACATTGCACCATGTATCGATACA
167889 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATTGCACCATGTATCGATACAG
Found at i:167957 original size:13 final size:13
Alignment explanation
Indices: 167939--167965 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
167929 ACAATTGTTC
167939 ATGTATCGATACA
1 ATGTATCGATACA
167952 ATGTATCGATACA
1 ATGTATCGATACA
167965 A
1 A
167966 AGAATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:168567 original size:47 final size:46
Alignment explanation
Indices: 168499--168651 Score: 132
Period size: 47 Copynumber: 3.5 Consensus size: 46
168489 AAGTTTTTAT
*
168499 TTTTCTCCCCCTTTATAAAAATTTTCCCCTTTAATTGGTTAAAGAGA
1 TTTTCTCCCCCTTGATAAAAATTTT-CCCTTTAATTGGTTAAAGAGA
* * *
168546 TTTTCTCCCCCTTGATAAAAA--TT--C--AAAGTT--TT----CGT
1 TTTTCTCCCCCTTGATAAAAATTTTCCCTTTAA-TTGGTTAAAGAGA
* *
168581 TTTTCTCCCCCTTTATAAAAATTTTCCTCTTTAATCGGTTAAAGAGA
1 TTTTCTCCCCCTTGATAAAAATTTTCC-CTTTAATTGGTTAAAGAGA
*
168628 TTTTCTCCCCCTAGATAAAAATTT
1 TTTTCTCCCCCTTGATAAAAATTT
168652 ATTTTCAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
35 21 0.26
37 2 0.02
39 2 0.02
40 3 0.04
41 3 0.04
42 3 0.04
43 2 0.02
45 2 0.02
47 43 0.53
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.42
Consensus pattern (46 bp):
TTTTCTCCCCCTTGATAAAAATTTTCCCTTTAATTGGTTAAAGAGA
Found at i:168623 original size:82 final size:82
Alignment explanation
Indices: 168481--168650 Score: 286
Period size: 82 Copynumber: 2.1 Consensus size: 82
168471 TAGAAAGTTC
* *
168481 AAATATCAAAGTTTTTATTTTTCTCCCCCTTTATAAAAATTTTCCCCTTTAATTGGTTAAAGAGA
1 AAAT-TCAAAGTTTTCATTTTTCTCCCCCTTTATAAAAATTTTCCCCTTTAATCGGTTAAAGAGA
*
168546 TTTTCTCCCCCTTGATAA
65 TTTTCTCCCCCTAGATAA
* *
168564 AAATTCAAAGTTTTCGTTTTTCTCCCCCTTTATAAAAATTTTCCTCTTTAATCGGTTAAAGAGAT
1 AAATTCAAAGTTTTCATTTTTCTCCCCCTTTATAAAAATTTTCCCCTTTAATCGGTTAAAGAGAT
168629 TTTCTCCCCCTAGATAA
66 TTTCTCCCCCTAGATAA
168646 AAATT
1 AAATT
168651 TATTTTCAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 78 0.95
83 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (82 bp):
AAATTCAAAGTTTTCATTTTTCTCCCCCTTTATAAAAATTTTCCCCTTTAATCGGTTAAAGAGAT
TTTCTCCCCCTAGATAA
Found at i:175773 original size:19 final size:19
Alignment explanation
Indices: 175745--175801 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
175735 TTGTATTGAT
* *
175745 ACATTATATCGATACATGT
1 ACATTGTATCGATACATGG
* *
175764 TCATTGTATCGATACACGG
1 ACATTGTATCGATACATGG
175783 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
175802 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:182050 original size:13 final size:13
Alignment explanation
Indices: 182032--182065 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
182022 ATATTCCTTA
182032 TATCGATACATTG
1 TATCGATACATTG
182045 TATCGATACATTG
1 TATCGATACATTG
*
182058 CATCGATA
1 TATCGATA
182066 TATGGGTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:182222 original size:21 final size:20
Alignment explanation
Indices: 182198--182236 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
182188 ACAAATTTCC
*
182198 TCATTTTTACTTCAAAATCCT
1 TCATTTTT-CATCAAAATCCT
182219 TCATTTTTCATCAAAATC
1 TCATTTTTCATCAAAATC
182237 ACCAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (20 bp):
TCATTTTTCATCAAAATCCT
Found at i:182286 original size:9 final size:9
Alignment explanation
Indices: 182274--182300 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
182264 AAATCGGTCT
182274 TTCAAAATC
1 TTCAAAATC
182283 TTCAAAATC
1 TTCAAAATC
182292 TTCAAAATC
1 TTCAAAATC
182301 CATTTTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (9 bp):
TTCAAAATC
Found at i:184055 original size:46 final size:47
Alignment explanation
Indices: 183969--184062 Score: 131
Period size: 46 Copynumber: 2.0 Consensus size: 47
183959 TTTATCTAGG
**
183969 TATCTATGGGGAGAAAATCTCTTTAACTGAATAAGGGGGAG-ATTTT
1 TATCTATGGGGAGAAAATCTCTTTAACTGAATAAAAGGGAGAATTTT
184015 TATCTA-GGGAGAGAAAATCTCTTTAACT-AATTAAAAGGGAGAATTTT
1 TATCTATGGG-GAGAAAATCTCTTTAACTGAA-TAAAAGGGAGAATTTT
184062 T
1 T
184063 TTTTAAGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
45 5 0.12
46 32 0.74
47 6 0.14
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (47 bp):
TATCTATGGGGAGAAAATCTCTTTAACTGAATAAAAGGGAGAATTTT
Found at i:184493 original size:22 final size:22
Alignment explanation
Indices: 184474--184516 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
184464 AAGTTTTAGA
184474 CTTATAAACAAATGTTTTTAAAC
1 CTTA-AAACAAATGTTTTTAAAC
*
184497 CTTAAATCAAATGTTTTTAA
1 CTTAAAACAAATGTTTTTAA
184517 GTAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (22 bp):
CTTAAAACAAATGTTTTTAAAC
Found at i:184661 original size:13 final size:13
Alignment explanation
Indices: 184643--184669 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
184633 ACATTATGCT
184643 TTGTATCGATACA
1 TTGTATCGATACA
184656 TTGTATCGATACA
1 TTGTATCGATACA
184669 T
1 T
184670 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:184666 original size:33 final size:32
Alignment explanation
Indices: 184624--184687 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
184614 CACACCCAGA
*
184624 TGTATCGATACAT-TATGCTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
184657 TGTATCGATACATGTTCATTGTATCGATACA
1 TGTATCGATACATGTTCATTGTATCGATACA
184688 CGGACAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:184678 original size:19 final size:19
Alignment explanation
Indices: 184653--184709 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
184643 TTGTATCGAT
*
184653 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
184672 TCATTGTATCGATACACGG
1 ACATTGTATCGATACATGG
184691 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
184710 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:184780 original size:33 final size:33
Alignment explanation
Indices: 184738--184806 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
184728 CTACCACTGT
*
184738 TTGTATCGATACATGGTACAA-TGTATCAATACA
1 TTGTATCGATACATGATA-AATTGTATCAATACA
*
184771 TTGTATCGATACATGATAAATTGTATCGATACA
1 TTGTATCGATACATGATAAATTGTATCAATACA
184804 TTG
1 TTG
184807 CTTCCAATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATAAATTGTATCAATACA
Found at i:186601 original size:13 final size:13
Alignment explanation
Indices: 186583--186607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186573 AGATTGCACA
186583 GTATCGATACATT
1 GTATCGATACATT
186596 GTATCGATACAT
1 GTATCGATACAT
186608 GACCAAATAT
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):
GTATCGATACATT
Found at i:186727 original size:13 final size:13
Alignment explanation
Indices: 186709--186734 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
186699 ACACACAATA
186709 TGTATCGATACAT
1 TGTATCGATACAT
186722 TGTATCGATACAT
1 TGTATCGATACAT
186735 CCCAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:186750 original size:33 final size:32
Alignment explanation
Indices: 186689--186756 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
186679 CCTTAACTGT
*
186689 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
186721 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
186754 TTG
1 TTG
186757 GCTTGTAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:192664 original size:8 final size:8
Alignment explanation
Indices: 192651--192676 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
192641 ATTTGATTAA
192651 ATTTTGTG
1 ATTTTGTG
192659 ATTTTGTG
1 ATTTTGTG
192667 ATTTTGTG
1 ATTTTGTG
192675 AT
1 AT
192677 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:192899 original size:13 final size:13
Alignment explanation
Indices: 192881--192916 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
192871 GAATTCTCTG
*
192881 TATCGATACATTA
1 TATCGATACAGTA
192894 TATCGATACAGTA
1 TATCGATACAGTA
192907 TATCGATACA
1 TATCGATACA
192917 AAGGGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (13 bp):
TATCGATACAGTA
Found at i:194812 original size:20 final size:21
Alignment explanation
Indices: 194782--194842 Score: 97
Period size: 20 Copynumber: 2.9 Consensus size: 21
194772 ATTGTTAAAT
194782 TATTTTATTAAGGGGGAGAAA
1 TATTTTATTAAGGGGGAGAAA
*
194803 -ATTTTTTTAAGGGGGAGAAA
1 TATTTTATTAAGGGGGAGAAA
194823 TTATTTTATTAAGGGGGAGA
1 -TATTTTATTAAGGGGGAGA
194843 GAAAAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 19 0.53
22 17 0.47
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (21 bp):
TATTTTATTAAGGGGGAGAAA
Found at i:194828 original size:22 final size:22
Alignment explanation
Indices: 194778--194842 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
194768 CGAAATTGTT
194778 AAATTATTTTATTAAGGGGGAG
1 AAATTATTTTATTAAGGGGGAG
*
194800 AAA--ATTTTTTTAAGGGGGAG
1 AAATTATTTTATTAAGGGGGAG
194820 AAATTATTTTATTAAGGGGGAG
1 AAATTATTTTATTAAGGGGGAG
194842 A
1 A
194843 GAAAAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.49
22 20 0.51
ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35
Consensus pattern (22 bp):
AAATTATTTTATTAAGGGGGAG
Found at i:195415 original size:13 final size:13
Alignment explanation
Indices: 195399--195423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
195389 AGATTACACA
195399 GTATCGATACATT
1 GTATCGATACATT
195412 GTATCGATACAT
1 GTATCGATACAT
195424 GACCAAATGT
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):
GTATCGATACATT
Found at i:195436 original size:20 final size:21
Alignment explanation
Indices: 195411--195463 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
195401 ATCGATACAT
*
195411 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
195431 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
195452 TGTATCGATACA
1 TGTATCGATACA
195464 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:196860 original size:33 final size:33
Alignment explanation
Indices: 196818--196886 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
196808 CCGTTGGAAG
*
196818 CAATGTATCGATACGATT-CATCATGCATCGATA
1 CAATGTATCGATAC-ATTGCACCATGCATCGATA
* *
196851 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGCACCATGCATCGATA
196884 CAA
1 CAA
196887 ACAGTGATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (33 bp):
CAATGTATCGATACATTGCACCATGCATCGATA
Found at i:196938 original size:20 final size:20
Alignment explanation
Indices: 196913--196965 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
196903 TACTGCCAGT
*
196913 TTCATGTATTGATACAATTA
1 TTCATGTATCGATACAATTA
*
196933 TTCATGTATCGATACAATGA
1 TTCATGTATCGATACAATTA
*
196953 -ACATGTATCGATA
1 TTCATGTATCGATA
196966 TAATGTATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TTCATGTATCGATACAATTA
Found at i:196959 original size:19 final size:20
Alignment explanation
Indices: 196915--196970 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
196905 CTGCCAGTTT
* * *
196915 CATGTATTGATACAATTATT
1 CATGTATCGATACAATGATA
196935 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
*
196954 CATGTATCGATATAATG
1 CATGTATCGATACAATG
196971 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:196977 original size:32 final size:33
Alignment explanation
Indices: 196936--196998 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
196926 ACAATTATTC
*
196936 ATGTATCGATACAATG-A-ACATGTATCGATATA
1 ATGTATCGATACAAAGCATA-ATGTATCGATATA
196968 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
196999 CATCTGGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATATA
Found at i:198032 original size:15 final size:17
Alignment explanation
Indices: 198012--198044 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
198002 TTGAAATATT
198012 TGAAAAT-TCT-TTTAA
1 TGAAAATGTCTATTTAA
198027 TGAAAATGTCTATTTAA
1 TGAAAATGTCTATTTAA
198044 T
1 T
198045 TCATGTCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (17 bp):
TGAAAATGTCTATTTAA
Done.