Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2477
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: 49748
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1621 original size:13 final size:13
Alignment explanation
Indices: 1603--1641 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1593 ACATTTTTCT
1603 TTGTATCGATACA
1 TTGTATCGATACA
1616 TTGTATCGATACA
1 TTGTATCGATACA
*
1629 CTGTATCGATACA
1 TTGTATCGATACA
1642 GGGGATTATA
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:3808 original size:13 final size:13
Alignment explanation
Indices: 3790--3815 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3780 TACACAAAGT
3790 ATGTATCGATACA
1 ATGTATCGATACA
3803 ATGTATCGATACA
1 ATGTATCGATACA
3816 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:3813 original size:32 final size:33
Alignment explanation
Indices: 3772--3833 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
3762 TAGCCAAACT
**
3772 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3804 TGTATCGATACACAAAAAATTGTATCGATA
1 TGTATCGATACACAAAAAATTGTATCGATA
3834 GATTGGCCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:4625 original size:28 final size:28
Alignment explanation
Indices: 4589--4794 Score: 349
Period size: 28 Copynumber: 7.3 Consensus size: 28
4579 TAAGCTTTCA
*
4589 GAAATGATGCCACTGACTTGTGGGCTTT
1 GAAAGGATGCCACTGACTTGTGGGCTTT
4617 GAAAGGATGCCACTGACTTGTGGGCTTT
1 GAAAGGATGCCACTGACTTGTGGGCTTT
*
4645 GAAAGGATGCCTCTGACTTGTGGGCTTT
1 GAAAGGATGCCACTGACTTGTGGGCTTT
*
4673 GAAAGGGTGCCACTGACTTGTGGGCTTT
1 GAAAGGATGCCACTGACTTGTGGGCTTT
*
4701 GAAAGGATGCCACTGACTTGTGAGCTTT
1 GAAAGGATGCCACTGACTTGTGGGCTTT
*
4729 GAAAAGAGTGCCACTGACTTGTGGGCTTT
1 GAAAGGA-TGCCACTGACTTGTGGGCTTT
*
4758 GAAAGGGTGCCACTGACTTGTGGGCTTT
1 GAAAGGATGCCACTGACTTGTGGGCTTT
4786 GAAAGGATG
1 GAAAGGATG
4795 AATGTTCTAG
Statistics
Matches: 166, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
28 141 0.85
29 25 0.15
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
GAAAGGATGCCACTGACTTGTGGGCTTT
Found at i:4793 original size:85 final size:84
Alignment explanation
Indices: 4596--4794 Score: 362
Period size: 85 Copynumber: 2.4 Consensus size: 84
4586 TCAGAAATGA
* * *
4596 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCTCTGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTGAAAAGATGCCACTGA
4661 CTTGTGGGCTTTGAAAGGG
66 CTTGTGGGCTTTGAAAGGG
4680 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTGAAAAGAGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTGAAAAGA-TGCCACTG
4745 ACTTGTGGGCTTTGAAAGGG
65 ACTTGTGGGCTTTGAAAGGG
4765 TGCCACTGACTTGTGGGCTTTGAAAGGATG
1 TGCCACTGACTTGTGGGCTTTGAAAGGATG
4795 AATGTTCTAG
Statistics
Matches: 111, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
84 54 0.49
85 57 0.51
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.29
Consensus pattern (84 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTGAAAAGATGCCACTGA
CTTGTGGGCTTTGAAAGGG
Found at i:5969 original size:1 final size:1
Alignment explanation
Indices: 5965--6025 Score: 68
Period size: 1 Copynumber: 61.0 Consensus size: 1
5955 CCTTTTTCTA
* * * * * *
5965 TTTTTTTGTTTTTTTTTCTTTTTGTTTTTGTTTTTTCTTTTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6026 GGGTGTGAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Found at i:16887 original size:34 final size:35
Alignment explanation
Indices: 16849--16915 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
16839 CCTTACAACA
16849 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
16883 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
16916 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:17392 original size:13 final size:13
Alignment explanation
Indices: 17374--17399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17364 CAATTTTTTG
17374 TGTATCGATACAT
1 TGTATCGATACAT
17387 TGTATCGATACAT
1 TGTATCGATACAT
17400 ACTTTGTGTA
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:17411 original size:32 final size:33
Alignment explanation
Indices: 17354--17417 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
17344 TATAAGCCAA
**
17354 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
17387 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
17418 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:19309 original size:13 final size:13
Alignment explanation
Indices: 19291--19315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19281 ACTGAAGCAA
19291 TGTATCGATACAT
1 TGTATCGATACAT
19304 TGTATCGATACA
1 TGTATCGATACA
19316 ATCTGGAAAA
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:23056 original size:13 final size:13
Alignment explanation
Indices: 23038--23063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23028 CAATTTTTTG
23038 TGTATCGATACAT
1 TGTATCGATACAT
23051 TGTATCGATACAT
1 TGTATCGATACAT
23064 ACTTTGTGTA
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:23075 original size:32 final size:33
Alignment explanation
Indices: 23018--23081 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
23008 TATAAGCCAA
**
23018 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
23051 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
23082 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:26881 original size:20 final size:20
Alignment explanation
Indices: 26856--26948 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
26846 GTAAAAAAAC
26856 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
26876 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
26896 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
26916 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
26936 AAAATGTATCGAT
1 AGAATGTATCGAT
26949 CTATCTAGGC
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
19 1 0.01
20 65 0.97
21 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:28809 original size:19 final size:20
Alignment explanation
Indices: 28761--28813 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
28751 CTGCCAGTTT
* **
28761 CATATATCGATACAATTGTC
1 CATATATCGATACAATCGAA
*
28781 CATGTATCGATACAA-CGAA
1 CATATATCGATACAATCGAA
28800 CATATATCGATACA
1 CATATATCGATACA
28814 TTATATCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (20 bp):
CATATATCGATACAATCGAA
Found at i:28877 original size:135 final size:135
Alignment explanation
Indices: 28720--29001 Score: 510
Period size: 135 Copynumber: 2.1 Consensus size: 135
28710 CAATGTGCCA
28720 TGTATCGATACAAATAGTGGTAGGGTAGCTACTGCCAGTTTCATATATCGATACAATTGTCCATG
1 TGTATCGATACAAATAGTGGTAGGGTAGCTACTGCCAGTTTCATATATCGATACAATTGTCCATG
28785 TATCGATACAACGAACATATATCGATACATTATATCAATACAAAGGATAATGTATCAATACATCT
66 TATCGATACAACGAACATATATCGATACATTATATCAATACAAAGGATAATGTATCAATACATCT
28850 AGGTG
131 AGGTG
*
28855 TGTATCGATACAAATAGTGGTAGGGTAGCTACTGCCAGTTTCATGTATCGATACAATTGTCCATG
1 TGTATCGATACAAATAGTGGTAGGGTAGCTACTGCCAGTTTCATATATCGATACAATTGTCCATG
* * * **
28920 TATCGATACAATGAACATATATCGATATATTGTATTGATACAAAGGATAATGTATCAATACATCT
66 TATCGATACAACGAACATATATCGATACATTATATCAATACAAAGGATAATGTATCAATACATCT
28985 AGGTG
131 AGGTG
28990 TGTATCGATACA
1 TGTATCGATACA
29002 TATAAGGGTT
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 141 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (135 bp):
TGTATCGATACAAATAGTGGTAGGGTAGCTACTGCCAGTTTCATATATCGATACAATTGTCCATG
TATCGATACAACGAACATATATCGATACATTATATCAATACAAAGGATAATGTATCAATACATCT
AGGTG
Found at i:28944 original size:19 final size:20
Alignment explanation
Indices: 28900--28946 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
28890 CAGTTTCATG
** *
28900 TATCGATACAATTGTCCATG
1 TATCGATACAATTGAACATA
28920 TATCGATACAA-TGAACATA
1 TATCGATACAATTGAACATA
28939 TATCGATA
1 TATCGATA
28947 TATTGTATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (20 bp):
TATCGATACAATTGAACATA
Found at i:29136 original size:22 final size:22
Alignment explanation
Indices: 29089--29141 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
29079 TATTTTTACT
** *
29089 TAAAAACATTTGATTTAAGGTT
1 TAAAAACATTTGATTTAAACTC
29111 TAAAAACATTTG-TTTATAACTC
1 TAAAAACATTTGATTTA-AACTC
29133 T-AAAACATT
1 TAAAAACATT
29142 CATTGATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (22 bp):
TAAAAACATTTGATTTAAACTC
Found at i:37621 original size:32 final size:33
Alignment explanation
Indices: 37565--37739 Score: 95
Period size: 32 Copynumber: 5.5 Consensus size: 33
37555 AAATTTCCCA
37565 AATGTATCGATACAAAGATCAATGTAT-GATAC
1 AATGTATCGATACAAAGATCAATGTATCGATAC
**
37597 AATGTATCGATACATTGAGT-AATGTATCGATAC
1 AATGTATCGATACAAAGA-TCAATGTATCGATAC
** * * * *
37630 -AT-T-TCCTTGGCAGTAGCTTC-A--TAACGATAC
1 AATGTATCGAT-ACA-AAG-ATCAATGTATCGATAC
* *
37660 ATTGTATCGATACAAA-A-CTTATGTATCGATAC
1 AATGTATCGATACAAAGATC-AATGTATCGATAC
*
37692 ATTGTATCGATACATAAG-T-ATATGTATCGATAC
1 AATGTATCGATACA-AAGATCA-ATGTATCGATAC
*
37725 ATTGTATCGATACAA
1 AATGTATCGATACAA
37740 CACTTATGTA
Statistics
Matches: 110, Mismatches: 16, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
28 1 0.01
30 12 0.11
31 5 0.05
32 55 0.50
33 37 0.34
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (33 bp):
AATGTATCGATACAAAGATCAATGTATCGATAC
Found at i:37672 original size:13 final size:13
Alignment explanation
Indices: 37654--37738 Score: 56
Period size: 13 Copynumber: 6.5 Consensus size: 13
37644 AGCTTCATAA
37654 CGATACATTGTAT
1 CGATACATTGTAT
37667 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
37686 CGATACATTGTAT
1 CGATACATTGTAT
37699 CGATACA---TA-
1 CGATACATTGTAT
* *
37708 AG-TATA-TGTAT
1 CGATACATTGTAT
37719 CGATACATTGTAT
1 CGATACATTGTAT
37732 CGATACA
1 CGATACA
37739 ACACTTATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 22
0.69 0.05 0.27
Matches are distributed among these distances:
8 3 0.05
9 1 0.02
10 4 0.07
11 1 0.02
12 3 0.05
13 29 0.51
15 2 0.04
16 2 0.04
17 2 0.04
19 10 0.18
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:37686 original size:19 final size:16
Alignment explanation
Indices: 37662--37757 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 16
37652 AACGATACAT
37662 TGTATCGATACAAAACTTA
1 TGTATCGATAC--AA-TTA
37681 TGTATCGATAC-A-T-
1 TGTATCGATACAATTA
37694 TGTATCGATACATAAGTATA
1 TGTATCGATAC--AA-T-TA
37714 TGTATCGATAC-A-T-
1 TGTATCGATACAATTA
37727 TGTATCGATACAACACTTA
1 TGTATCGATAC-A-A-TTA
37746 TGTATCGATACA
1 TGTATCGATACA
37758 GTTACTTGTT
Statistics
Matches: 64, Mismatches: 0, Indels: 27
0.70 0.00 0.30
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 3 0.05
17 1 0.02
18 2 0.03
19 23 0.36
20 11 0.17
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (16 bp):
TGTATCGATACAATTA
Found at i:37753 original size:32 final size:31
Alignment explanation
Indices: 37654--37757 Score: 163
Period size: 32 Copynumber: 3.2 Consensus size: 31
37644 AGCTTCATAA
37654 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATAC-AAACTTATGTAT
*
37686 CGATACATTGTATCGATACATAAGTATATGTAT
1 CGATACATTGTATCGATACA-AACT-TATGTAT
37719 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAA-ACTTATGTAT
37751 CGATACA
1 CGATACA
37758 GTTACTTGTT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.01
32 37 0.55
33 29 0.43
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (31 bp):
CGATACATTGTATCGATACAAACTTATGTAT
Found at i:41310 original size:20 final size:19
Alignment explanation
Indices: 41268--41321 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
41258 GTTTAAAGCA
41268 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCA-C
41288 ATGTATCGATACAATGTGC-C
1 ATGTATCGATACAAT-T-CAC
*
41308 ATGTATTGATACAA
1 ATGTATCGATACAA
41322 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATTCAC
Found at i:41394 original size:19 final size:19
Alignment explanation
Indices: 41350--41405 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
41340 CTGCTAGTTT
* **
41350 CATGTATCGATACAATTGTC
1 CATGTATCGATATAA-TGAA
41370 CATGTATCGATATAATGAA
1 CATGTATCGATATAATGAA
41389 CATGTATCGATATAATG
1 CATGTATCGATATAATG
41406 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (19 bp):
CATGTATCGATATAATGAA
Found at i:41809 original size:7 final size:7
Alignment explanation
Indices: 41797--41839 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
41787 ATTATCAAAG
41797 TCAACAA
1 TCAACAA
41804 TCAACAA
1 TCAACAA
41811 TCAACAA
1 TCAACAA
*
41818 TCAA-AG
1 TCAACAA
*
41824 TCAATAA
1 TCAACAA
41831 TCAA-AA
1 TCAACAA
41837 TCA
1 TCA
41840 GTAGTCAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 10 0.30
7 23 0.70
ACGTcount: A:0.56, C:0.23, G:0.02, T:0.19
Consensus pattern (7 bp):
TCAACAA
Found at i:41816 original size:14 final size:13
Alignment explanation
Indices: 41790--41839 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
41780 AATTTTTATT
*
41790 ATCAAAGTCAACA
1 ATCAAAATCAACA
41803 ATCAACAATCAACA
1 ATCAA-AATCAACA
* *
41817 ATCAAAGTCAATA
1 ATCAAAATCAACA
41830 ATCAAAATCA
1 ATCAAAATCA
41840 GTAGTCAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 20 0.62
14 12 0.38
ACGTcount: A:0.56, C:0.22, G:0.04, T:0.18
Consensus pattern (13 bp):
ATCAAAATCAACA
Found at i:41827 original size:20 final size:20
Alignment explanation
Indices: 41804--41850 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
41794 AAGTCAACAA
41804 TCAACAATCAACAATCA-AAG
1 TCAACAATCAA-AATCAGAAG
* *
41824 TCAATAATCAAAATCAGTAG
1 TCAACAATCAAAATCAGAAG
41844 TCAACAA
1 TCAACAA
41851 GTAAAGTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.53, C:0.21, G:0.06, T:0.19
Consensus pattern (20 bp):
TCAACAATCAAAATCAGAAG
Found at i:41839 original size:33 final size:34
Alignment explanation
Indices: 41797--41864 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 34
41787 ATTATCAAAG
41797 TCAACAATCAACAATCAACAA-TCAAAGTCAATAA
1 TCAACAATCAACAATCAACAAGT-AAAGTCAATAA
** *
41831 TCAA-AATCAGTAGTCAACAAGTAAAGTCAATAA
1 TCAACAATCAACAATCAACAAGTAAAGTCAATAA
41864 T
1 T
41865 TAACGTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21
Consensus pattern (34 bp):
TCAACAATCAACAATCAACAAGTAAAGTCAATAA
Found at i:43648 original size:18 final size:16
Alignment explanation
Indices: 43625--43659 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
43615 TTATCATAGG
43625 TTTAAGTTGTATTTCTTT
1 TTTAAGTT-TATTT-TTT
43643 TTTAAGTTTATTTTTT
1 TTTAAGTTTATTTTTT
43659 T
1 T
43660 AGTTGTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (16 bp):
TTTAAGTTTATTTTTT
Found at i:45196 original size:21 final size:19
Alignment explanation
Indices: 45171--45217 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
45161 TAAGATGATT
* *
45171 AAAATATGAAAATTTATTATA
1 AAAATATAAAAAATT-TTA-A
45192 AAAAT-TAAAAAATTTTAA
1 AAAATATAAAAAATTTTAA
45210 AAAATATA
1 AAAATATA
45218 TTTTGGCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.26
19 5 0.22
20 7 0.30
21 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATATAAAAAATTTTAA
Found at i:47781 original size:30 final size:30
Alignment explanation
Indices: 47741--47797 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
47731 TAAAAATGAT
*
47741 TAAAATTATATTTATATTAAATAATAAAAA
1 TAAAAATATATTTATATTAAATAATAAAAA
*
47771 TAAAAATATATTTATATTGAATAATAA
1 TAAAAATATATTTATATTAAATAATAA
47798 TTAACAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TAAAAATATATTTATATTAAATAATAAAAA
Found at i:47874 original size:25 final size:24
Alignment explanation
Indices: 47811--47874 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
47801 ACAATTATTA
*
47811 ATTATATTTATAGTAAAAATAAATT
1 ATTATA-TTATATTAAAAATAAATT
* *
47836 ATTATATTAGATTAACAACTAAA-T
1 ATTATATTATATTAA-AAATAAATT
47860 ATTATATTAATATTA
1 ATTATATT-ATATTA
47875 TATAATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (24 bp):
ATTATATTATATTAAAAATAAATT
Found at i:48590 original size:16 final size:16
Alignment explanation
Indices: 48569--48599 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48559 TGAATTGAAT
*
48569 AATCTAAATTCAAAAG
1 AATCTAAATCCAAAAG
48585 AATCTAAATCCAAAA
1 AATCTAAATCCAAAA
48600 AAATTCAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.23
Consensus pattern (16 bp):
AATCTAAATCCAAAAG
Found at i:48870 original size:24 final size:23
Alignment explanation
Indices: 48826--48870 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
48816 TATGAAAATG
*
48826 TATTTATAATTATCATACAATTA
1 TATTTATAATTATAATACAATTA
48849 TATTTAATAATATATAAT-CAAT
1 TATTT-ATAAT-TATAATACAAT
48871 AAAGATATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 9 0.47
25 5 0.26
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTATAATTATAATACAATTA
Found at i:49298 original size:21 final size:22
Alignment explanation
Indices: 49273--49315 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
49263 CTTATAACTA
49273 AAAT-ATAAAGATTAAAA-AATT
1 AAATAATAAA-ATTAAAACAATT
*
49294 AAATAATTAAATTAAAACAATT
1 AAATAATAAAATTAAAACAATT
49316 TCAACCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATAATAAAATTAAAACAATT
Done.