Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1744
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: 55095
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1398 original size:34 final size:34
Alignment explanation
Indices: 1329--1546 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
1319 AAGTGGGAGA
* * *
1329 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1362 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1396 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1429 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1463 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1497 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1531 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1547 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1512 original size:68 final size:67
Alignment explanation
Indices: 1329--1548 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
1319 AAGTGGGAGA
* * * * *
1329 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1394 CC
66 CC
* * * *
1396 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1461 CC
66 CC
* * *
1463 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
1528 GCC
65 GCC
1531 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1549 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:3881 original size:8 final size:8
Alignment explanation
Indices: 3868--3899 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
3858 TTATGTATGA
3868 ATATTTAT
1 ATATTTAT
3876 ATATTTAT
1 ATATTTAT
3884 ATATTT-T
1 ATATTTAT
3891 AT-TTTAT
1 ATATTTAT
3898 AT
1 AT
3900 TTATTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
6 3 0.13
7 6 0.26
8 14 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATATTTAT
Found at i:4061 original size:21 final size:23
Alignment explanation
Indices: 4024--4066 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
4014 AATTATATAT
*
4024 AATAAATATATATTATT-TTAAA
1 AATAAATATAAATTATTATTAAA
4046 AATAAA-ATAAATTATTATTAA
1 AATAAATATAAATTATTATTAA
4067 TTAAATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAAATATAAATTATTATTAAA
Found at i:4138 original size:22 final size:22
Alignment explanation
Indices: 4108--4167 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
4098 TTTTATTTTC
4108 AAATATAATTATAAAAAAAATAA
1 AAAT-TAATTATAAAAAAAATAA
* *
4131 AAATTAATAAT-AAAAAATTAA
1 AAATTAATTATAAAAAAAATAA
4152 AAATTAATT-TAAAAAA
1 AAATTAATTATAAAAAA
4168 TTAAATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 22 0.67
22 6 0.18
23 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATTAATTATAAAAAAAATAA
Found at i:4147 original size:21 final size:20
Alignment explanation
Indices: 4121--4183 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
4111 TATAATTATA
*
4121 AAAAAAATAAAAATTAATAAT
1 AAAAAATTAAAAATTAAT-AT
*
4142 AAAAAATTAAAAATTAATTT
1 AAAAAATTAAAAATTAATAT
4162 AAAAAATT--AAATTAA-AT
1 AAAAAATTAAAAATTAATAT
4179 AAAAA
1 AAAAA
4184 TCTTAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
17 6 0.15
18 7 0.18
20 9 0.23
21 17 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAAATTAAAAATTAATAT
Found at i:4169 original size:20 final size:21
Alignment explanation
Indices: 4114--4172 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
4104 TTTCAAATAT
4114 AATT-ATAA-AAAAAA-TAAA
1 AATTAATAATAAAAAATTAAA
4132 AATTAATAATAAAAAATTAAA
1 AATTAATAATAAAAAATTAAA
*
4153 AATTAAT-TTAAAAAATTAAA
1 AATTAATAATAAAAAATTAAA
4173 TTAAATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 4 0.11
19 4 0.11
20 18 0.49
21 11 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTAATAATAAAAAATTAAA
Found at i:4238 original size:21 final size:21
Alignment explanation
Indices: 4212--4260 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
4202 TTTTATACCG
*
4212 ATCAATACTTTCTTGATATAA
1 ATCAATACTTACTTGATATAA
*
4233 ATCAATACTTACTTGATATAG
1 ATCAATACTTACTTGATATAA
4254 ATCAATA
1 ATCAATA
4261 AAAACCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (21 bp):
ATCAATACTTACTTGATATAA
Found at i:7726 original size:3 final size:3
Alignment explanation
Indices: 7718--7764 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
7708 CAAAAAATTA
*
7718 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7765 CATGTGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:11899 original size:23 final size:24
Alignment explanation
Indices: 11865--11913 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
11855 TATAAAAAAA
*
11865 TAACTAATCATTC-AAAAAATACC
1 TAACTAACCATTCAAAAAAATACC
11888 TAACTAACCATTCAAAAAAATACC
1 TAACTAACCATTCAAAAAAATACC
11912 TA
1 TA
11914 CTTATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.24
Consensus pattern (24 bp):
TAACTAACCATTCAAAAAAATACC
Found at i:12034 original size:16 final size:17
Alignment explanation
Indices: 12015--12046 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12005 AAAATATTAA
12015 ATAAAT-AATTTAATTT
1 ATAAATAAATTTAATTT
12031 ATAAATAAATTTAATT
1 ATAAATAAATTTAATT
12047 AGATGCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATAAATTTAATTT
Found at i:16122 original size:31 final size:31
Alignment explanation
Indices: 16084--16142 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
16074 AAATACTTGA
*
16084 ATTATTTCATGAACAAAGTCATTCGAATCGC
1 ATTATTTCATGAACAAAGCCATTCGAATCGC
* *
16115 ATTATTTCATGCACATAGCCATTCGAAT
1 ATTATTTCATGAACAAAGCCATTCGAAT
16143 GGCACCGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (31 bp):
ATTATTTCATGAACAAAGCCATTCGAATCGC
Found at i:17797 original size:24 final size:24
Alignment explanation
Indices: 17748--17799 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
17738 GAAAAATAAT
* *
17748 TAAAATAAAAAATAATATATTTTA
1 TAAAATAAAAAATAATATAATATA
17772 TAAAAT-AAAAATAATATAAATATA
1 TAAAATAAAAAATAATAT-AATATA
17796 TAAA
1 TAAA
17800 TATATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAATAAAAAATAATATAATATA
Found at i:18063 original size:4 final size:4
Alignment explanation
Indices: 18054--18079 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18044 AAAAAATAAC
18054 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
18080 GACTGGCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:18743 original size:28 final size:28
Alignment explanation
Indices: 18697--18759 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
18687 AAATATTATA
* * *
18697 TTTTTATAAAAGATGATATCTATACATC
1 TTTTTATAAAAAATAATATCTATACACC
* *
18725 TTTTTATAAAAAATAATATTTATATACC
1 TTTTTATAAAAAATAATATCTATACACC
18753 TTTTTAT
1 TTTTTAT
18760 CTAAGATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (28 bp):
TTTTTATAAAAAATAATATCTATACACC
Found at i:20639 original size:18 final size:21
Alignment explanation
Indices: 20602--20641 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
20592 AATTTAATTA
20602 TTAAAATATATAAATATTTAT
1 TTAAAATATATAAATATTTAT
20623 TTAAAA-ATA-AAAT-TTTAT
1 TTAAAATATATAAATATTTAT
20641 T
1 T
20642 AATATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 3 0.16
21 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAAATATATAAATATTTAT
Found at i:21083 original size:94 final size:94
Alignment explanation
Indices: 20911--21089 Score: 234
Period size: 94 Copynumber: 1.9 Consensus size: 94
20901 AAATAGATCA
* * *
20911 TTTTTAAAAATTACCCATTTTAAACTAATAAAGTAATAAATATACATATTTATAAGTTAGATCGT
1 TTTTTAAAAATTACCCATTTTAAACTAATAAAATAATAAATATACATATTTATAAATTAGATCAT
* *
20976 AATTTGAATATTTTAAATTTTTTAAATTT
66 AACTTGAACATTTTAAATTTTTTAAATTT
* * * * * *
21005 TTTTTAAAAATTACTCATTTTAAGCTAATAAAATAATAAATATATATGTTTGTAAATTA-AGTTA
1 TTTTTAAAAATTACCCATTTTAAACTAATAAAATAATAAATATACATATTTATAAATTAGA-TCA
*
21069 TAACTTGAGCATTTTAAATTT
65 TAACTTGAACATTTTAAATTT
21090 CTTTTTTTAA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
93 1 0.01
94 71 0.99
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (94 bp):
TTTTTAAAAATTACCCATTTTAAACTAATAAAATAATAAATATACATATTTATAAATTAGATCAT
AACTTGAACATTTTAAATTTTTTAAATTT
Found at i:21934 original size:18 final size:17
Alignment explanation
Indices: 21877--21954 Score: 63
Period size: 18 Copynumber: 4.5 Consensus size: 17
21867 AAATAAGGAA
*
21877 GAAGAAGAGGAGGAAAT
1 GAAGAAGAAGAGGAAAT
* * *
21894 GGAAGATGATGATGATGAA-
1 -GAAGAAGAAGAGGA--AAT
21913 GAAGAAGAAGAGGAAGAT
1 GAAGAAGAAGAGGAA-AT
21931 GAAGAAGAAG-GGAAA-
1 GAAGAAGAAGAGGAAAT
21946 GAAGAAGAA
1 GAAGAAGAA
21955 AATGGTGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
15 9 0.18
16 2 0.04
17 5 0.10
18 32 0.64
20 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.38, T:0.08
Consensus pattern (17 bp):
GAAGAAGAAGAGGAAAT
Found at i:23809 original size:1 final size:1
Alignment explanation
Indices: 23805--23829 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
23795 TTTTAATTTG
23805 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
23830 CTCCATACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25701 original size:6 final size:6
Alignment explanation
Indices: 25690--25784 Score: 136
Period size: 6 Copynumber: 15.8 Consensus size: 6
25680 GCGGAAGATT
* * * * *
25690 TCTCTG TCTCTG TCTCTC TCTCTG TCTCTC TCTCTG TCTCTC TGTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
*
25738 TCTCTG TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCT
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCT
25785 TTTGCTATGT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 80 1.00
ACGTcount: A:0.00, C:0.43, G:0.06, T:0.51
Consensus pattern (6 bp):
TCTCTC
Found at i:25717 original size:8 final size:8
Alignment explanation
Indices: 25690--25784 Score: 136
Period size: 8 Copynumber: 11.9 Consensus size: 8
25680 GCGGAAGATT
*
25690 TCTCTGTC
1 TCTCTCTC
*
25698 TCTGTCTC
1 TCTCTCTC
*
25706 TCTCTCTG
1 TCTCTCTC
25714 TCTCTCTC
1 TCTCTCTC
*
25722 TCTGTCTC
1 TCTCTCTC
*
25730 TCTGTCTC
1 TCTCTCTC
*
25738 TCTCTGTC
1 TCTCTCTC
25746 TCTCTCTC
1 TCTCTCTC
25754 TCTCTCTC
1 TCTCTCTC
25762 TCTCTCTC
1 TCTCTCTC
25770 TCTCTCTC
1 TCTCTCTC
25778 TCTCTCT
1 TCTCTCT
25785 TTTGCTATGT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 78 1.00
ACGTcount: A:0.00, C:0.43, G:0.06, T:0.51
Consensus pattern (8 bp):
TCTCTCTC
Found at i:33621 original size:13 final size:15
Alignment explanation
Indices: 33590--33623 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
33580 TAATTTTTTA
33590 AAATAAAATAAACTT
1 AAATAAAATAAACTT
33605 AAATAAAA-AAA-TT
1 AAATAAAATAAACTT
33618 AAATAA
1 AAATAA
33624 GTACATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 3 0.16
15 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAATAAACTT
Found at i:33683 original size:18 final size:19
Alignment explanation
Indices: 33656--33696 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
33646 AAAATATTTT
33656 TTAAAATTTAATTTT-AAA
1 TTAAAATTTAATTTTAAAA
* *
33674 TTAAATTTTACTTTTAAAA
1 TTAAAATTTAATTTTAAAA
33693 TTAA
1 TTAA
33697 TTTAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATTTAATTTTAAAA
Found at i:33725 original size:15 final size:15
Alignment explanation
Indices: 33707--33744 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
33697 TTTAATATGA
33707 TTAAATAAAATAAAT
1 TTAAATAAAATAAAT
33722 TTAAAT-AAATAAAT
1 TTAAATAAAATAAAT
33736 TT-AATAAAA
1 TTAAATAAAA
33745 ATATGATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 13 0.59
15 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAATAAAATAAAT
Found at i:33928 original size:21 final size:22
Alignment explanation
Indices: 33902--33954 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
33892 AATTGATATA
33902 TATATATAATTGA-TTTAATTT
1 TATATATAATTGATTTTAATTT
*
33923 TATATA-ATATTTATTTTAATTT
1 TATATATA-ATTGATTTTAATTT
*
33945 TA-ATTTAATT
1 TATATATAATT
33955 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 15 0.56
22 11 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATATATAATTGATTTTAATTT
Found at i:33934 original size:17 final size:18
Alignment explanation
Indices: 33904--33940 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
33894 TTGATATATA
33904 TATATAATTGATTTAATTT
1 TATATAATTGATTT-ATTT
33923 TATATAA-T-ATTTATTT
1 TATATAATTGATTTATTT
33939 TA
1 TA
33941 ATTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 1 0.06
19 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TATATAATTGATTTATTT
Found at i:33946 original size:11 final size:10
Alignment explanation
Indices: 33914--33956 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 10
33904 TATATAATTG
33914 ATTTAATTTT
1 ATTTAATTTT
*
33924 ATATAATATTT
1 ATTTAAT-TTT
33935 ATTTTAATTTT
1 A-TTTAATTTT
33946 AATTTAATTTT
1 -ATTTAATTTT
33957 TTAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 6 0.21
11 16 0.57
12 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTAATTTT
Found at i:33976 original size:19 final size:19
Alignment explanation
Indices: 33954--34014 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
33944 TTAATTTAAT
33954 TTTTTAAAAAATTAAAATA
1 TTTTTAAAAAATTAAAATA
* *
33973 -TTTTATCATAATTAAAATA
1 TTTTTA-AAAAATTAAAATA
* *
33992 TTTTTAAAAAAATAAATTA
1 TTTTTAAAAAATTAAAATA
34011 TTTT
1 TTTT
34015 CACCCTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 5 0.15
19 24 0.71
20 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTTTAAAAAATTAAAATA
Found at i:40902 original size:67 final size:67
Alignment explanation
Indices: 40794--40927 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
40784 TGGAATAGAA
40794 AGGCAATCACATAAACAACCTTCTAAATGGAACACCTGCTACAATTTTAGAATGTAATTTAGATG
1 AGGCAATCACATAAACAACCTTCTAAATGGAACACCTGCTACAATTTTAGAATGTAATTTAGATG
40859 AT
66 AT
40861 AGGCAATCACATAAACAACCTTCTAAATGGAACACCTGCTACAATTTTAGAATGTAATTTAGATG
1 AGGCAATCACATAAACAACCTTCTAAATGGAACACCTGCTACAATTTTAGAATGTAATTTAGATG
40926 AT
66 AT
40928 GCCACCAAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (67 bp):
AGGCAATCACATAAACAACCTTCTAAATGGAACACCTGCTACAATTTTAGAATGTAATTTAGATG
AT
Found at i:43123 original size:17 final size:18
Alignment explanation
Indices: 43101--43136 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
43091 CTAAGCAATT
43101 TTTTATTT-AAAATAAAA
1 TTTTATTTGAAAATAAAA
*
43118 TTTTATTTGAATATAAAA
1 TTTTATTTGAAAATAAAA
43136 T
1 T
43137 AAAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTATTTGAAAATAAAA
Found at i:43639 original size:20 final size:18
Alignment explanation
Indices: 43597--43645 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
43587 ATAAAAAATT
*
43597 AATTTTTAAATATTTTAA
1 AATTTTTAAATATATTAA
*
43615 TATTTTTAAATAATAATTAA
1 AATTTTTAAAT-AT-ATTAA
*
43635 AATTTTCAAAT
1 AATTTTTAAAT
43646 CAAACTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 2 0.08
20 13 0.52
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTTTAAATATATTAA
Found at i:44617 original size:21 final size:22
Alignment explanation
Indices: 44585--44627 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
44575 AAATTAAAAA
* *
44585 ATATATTTTTATGATAATATTT
1 ATATATTTTTATAATAAAATTT
44607 ATATA-TTTTATAATAAAATTT
1 ATATATTTTTATAATAAAATTT
44628 TAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATTTTTATAATAAAATTT
Found at i:47278 original size:37 final size:35
Alignment explanation
Indices: 47237--47314 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 35
47227 TATTTTATTT
*
47237 TTTAAATGTAAAAATATTTT-TATATTTTATAATTAAA
1 TTTAAATATAAAAATATTTTAT-TA-TTTA-AATTAAA
*
47274 TTTAAATATAAATATATTTTATTATTTAAATTAAA
1 TTTAAATATAAAAATATTTTATTATTTAAATTAAA
47309 -TTAAAT
1 TTTAAAT
47315 TATTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
34 6 0.16
35 7 0.18
36 4 0.11
37 20 0.53
38 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
TTTAAATATAAAAATATTTTATTATTTAAATTAAA
Found at i:47326 original size:29 final size:30
Alignment explanation
Indices: 47257--47321 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
47247 AAAATATTTT
*
47257 TATATTTTA-TAATTAAATTTAAATATAAA
1 TATATTTTATTATTTAAATTTAAATATAAA
47286 TATATTTTATTATTTAAA-TTAAAT-TAAA
1 TATATTTTATTATTTAAATTTAAATATAAA
47314 T-TATTTTA
1 TATATTTTA
47322 AATTAGTGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.21
28 5 0.15
29 15 0.44
30 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TATATTTTATTATTTAAATTTAAATATAAA
Found at i:47414 original size:3 final size:3
Alignment explanation
Indices: 47406--47430 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
47396 TGAAGAAAGC
47406 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
47431 GAAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:48352 original size:3 final size:3
Alignment explanation
Indices: 48346--48378 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
48336 AAAATAACAT
48346 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48379 GAAAAAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:50326 original size:60 final size:60
Alignment explanation
Indices: 50245--50362 Score: 200
Period size: 60 Copynumber: 2.0 Consensus size: 60
50235 GGTGATGAGC
* * *
50245 TGGATTCCTCTCTGGTTTCCTCTTGGAAACATGCTGCAGATGATGAGGATGATGGTGAAT
1 TGGATTCCTCTCTCGTGTCCTCTTGGAAACATGCTGCAAATGATGAGGATGATGGTGAAT
*
50305 TGGATTCTTCTCTCGTGTCCTCTTGGAAACATGCTGCAAATGATGAGGATGATGGTGA
1 TGGATTCCTCTCTCGTGTCCTCTTGGAAACATGCTGCAAATGATGAGGATGATGGTGA
50363 TGGCGTTGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (60 bp):
TGGATTCCTCTCTCGTGTCCTCTTGGAAACATGCTGCAAATGATGAGGATGATGGTGAAT
Done.