Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_465
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: 69127
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1700 original size:16 final size:16
Alignment explanation
Indices: 1676--1713 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1666 ATAGCTGGAC
*
1676 TTTCTACTTTTCGGCA
1 TTTCGACTTTTCGGCA
*
1692 TTTCGACTTTTTGGCA
1 TTTCGACTTTTCGGCA
1708 TTTCGA
1 TTTCGA
1714 GATTTGTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (16 bp):
TTTCGACTTTTCGGCA
Found at i:6731 original size:18 final size:18
Alignment explanation
Indices: 6691--6731 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6681 CTTGGCCCAT
6691 TGCAGTAACAGTAAATAG
1 TGCAGTAACAGTAAATAG
*
6709 AGCAGTAACAGT-AATCAG
1 TGCAGTAACAGTAAAT-AG
6727 TGCAG
1 TGCAG
6732 CCAATGAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (18 bp):
TGCAGTAACAGTAAATAG
Found at i:9568 original size:56 final size:56
Alignment explanation
Indices: 9463--9569 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
9453 ATTAATGCTG
* * * * *
9463 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
9519 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
9570 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:10217 original size:20 final size:20
Alignment explanation
Indices: 10192--10246 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
10182 ACGAGTTAAA
* *
10192 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
10212 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
10232 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
10247 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:11569 original size:15 final size:16
Alignment explanation
Indices: 11530--11570 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
11520 AACAACACTC
11530 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
11546 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
11560 CTTTCTTTTTC
1 CTTTCTTTTTC
11571 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:11765 original size:17 final size:15
Alignment explanation
Indices: 11728--11766 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
11718 TATCTCCCAC
11728 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
11744 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
11761 TCATTT
1 TCATTT
11767 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:12651 original size:13 final size:13
Alignment explanation
Indices: 12635--12659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12625 TCAATTTCGA
12635 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
12648 TTTTTTTTCTTC
1 TTTTTTTTCTTC
12660 AATACTAAAT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:14102 original size:56 final size:55
Alignment explanation
Indices: 13986--14103 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
13976 TGCATGCTTT
* * * *
13986 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
14040 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
14096 CATTAAAT
1 CATTAAAT
14104 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:14752 original size:20 final size:20
Alignment explanation
Indices: 14727--14781 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
14717 ACGAGTTAAA
* *
14727 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
14747 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
14767 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
14782 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:16271 original size:13 final size:13
Alignment explanation
Indices: 16253--16277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16243 TGGTCATCAT
16253 GGTGTGAACACAA
1 GGTGTGAACACAA
16266 GGTGTGAACACA
1 GGTGTGAACACA
16278 TGATCAATAC
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:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:18128 original size:17 final size:18
Alignment explanation
Indices: 18106--18139 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18096 ACAACACTCC
*
18106 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
18123 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
18140 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:18247 original size:15 final size:16
Alignment explanation
Indices: 18222--18253 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
18212 TATCTCACAC
18222 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
18238 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
18253 T
1 T
18254 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:19219 original size:16 final size:16
Alignment explanation
Indices: 19181--19223 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
19171 TTTTTAACTT
*
19181 GATTTTTTTTTTGGTC
1 GATTTTTTTTTTGCTC
*
19197 -ACCTTTTTTTTTGCTC
1 GA-TTTTTTTTTTGCTC
19213 GATTTTTTTTT
1 GATTTTTTTTT
19224 CACTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.07, C:0.12, G:0.12, T:0.70
Consensus pattern (16 bp):
GATTTTTTTTTTGCTC
Found at i:19231 original size:13 final size:13
Alignment explanation
Indices: 19215--19278 Score: 74
Period size: 13 Copynumber: 4.6 Consensus size: 13
19205 TTTTGCTCGA
*
19215 TTTTTTTTTCACT
1 TTTTTTTTTCAAT
*
19228 TTTTTTTTTGAAT
1 TTTTTTTTTCAAT
19241 TTTTTTTTCAATCAAT
1 TTTTTTTT---TCAAT
19257 TTTTTTTTTCGAAT
1 TTTTTTTTTC-AAT
19271 TTTTTTTT
1 TTTTTTTT
19279 GATTTTTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 21 0.48
14 11 0.25
16 12 0.27
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:19244 original size:14 final size:14
Alignment explanation
Indices: 19227--19278 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
19217 TTTTTTTCAC
19227 TTTTTTTTTTGAAT
1 TTTTTTTTTTGAAT
* *
19241 TTTTTTTTCAATCAAT
1 TTTTTTTT--TTGAAT
*
19257 TTTTTTTTTCGAAT
1 TTTTTTTTTTGAAT
19271 TTTTTTTT
1 TTTTTTTT
19279 GATTTTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 19 0.61
16 12 0.39
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTTGAAT
Found at i:19283 original size:11 final size:13
Alignment explanation
Indices: 19201--19287 Score: 65
Period size: 13 Copynumber: 6.5 Consensus size: 13
19191 TTGGTCACCT
19201 TTTTTTTTGCTCG-A
1 TTTTTTTT--TCGAA
*
19215 TTTTTTTTTC-AC
1 TTTTTTTTTCGAA
*
19227 TTTTTTTTTTGAA
1 TTTTTTTTTCGAA
*
19240 TTTTTTTTTCAATCAA
1 TTTTTTTTTC---GAA
19256 TTTTTTTTTTCGAA
1 -TTTTTTTTTCGAA
19270 TTTTTTTTT-G-A
1 TTTTTTTTTCGAA
19281 TTTTTTT
1 TTTTTTT
19288 GTTACTCCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
11 8 0.13
12 12 0.20
13 19 0.31
14 10 0.16
16 2 0.03
17 10 0.16
ACGTcount: A:0.13, C:0.08, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:20344 original size:13 final size:13
Alignment explanation
Indices: 20326--20350 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20316 TGGTCATCAT
20326 GGTGTGAACACAA
1 GGTGTGAACACAA
20339 GGTGTGAACACA
1 GGTGTGAACACA
20351 TGATCAATAC
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:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:21785 original size:15 final size:16
Alignment explanation
Indices: 21746--21786 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
21736 AACAACACTC
21746 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
21762 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
21776 CTTTCTTTTTC
1 CTTTCTTTTTC
21787 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:24456 original size:25 final size:26
Alignment explanation
Indices: 24410--24458 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
24400 AATCACTCTT
* * *
24410 TTTTTTTTCAATTTCGATTTTTTTCC
1 TTTTTTTTCAATTCCAAATTTTTTCC
24436 TTTTTTTT-AATTCCAAATTTTTT
1 TTTTTTTTCAATTCCAAATTTTTT
24459 TTCTTCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTTTTTCAATTCCAAATTTTTTCC
Found at i:24536 original size:12 final size:12
Alignment explanation
Indices: 24514--24550 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
24504 AAATTGAATA
24514 CAAACTTTTTTTT
1 CAAA-TTTTTTTT
24527 CAAATTTTTTTT
1 CAAATTTTTTTT
*
24539 CAAGTTTTTTTT
1 CAAATTTTTTTT
24551 ATTTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.65
Consensus pattern (12 bp):
CAAATTTTTTTT
Found at i:27008 original size:22 final size:22
Alignment explanation
Indices: 26980--27023 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
26970 TTTTGAACCA
*
26980 TTACCATTTCTTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
27002 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
27024 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.36, G:0.02, T:0.36
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:27558 original size:22 final size:22
Alignment explanation
Indices: 27528--27571 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27518 TTTGGTATTT
27528 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
27550 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
27572 TGTTCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:28125 original size:10 final size:10
Alignment explanation
Indices: 28110--28147 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
28100 GCTCATTTCC
*
28110 AGCTCACTCG
1 AGCTCAATCG
28120 AGCTCAAGTC-
1 AGCTCAA-TCG
28130 AGCTCAATCG
1 AGCTCAATCG
28140 AGCTCAAT
1 AGCTCAAT
28148 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:28134 original size:20 final size:20
Alignment explanation
Indices: 28109--28146 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28099 AGCTCATTTC
*
28109 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
28129 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
28147 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:28153 original size:20 final size:20
Alignment explanation
Indices: 28110--28170 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
28100 GCTCATTTCC
* * *
28110 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
28130 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
28150 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
28170 A
1 A
28171 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:28164 original size:11 final size:10
Alignment explanation
Indices: 28120--28166 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
28110 AGCTCACTCG
*
28120 AGCTCAAGTC
1 AGCTCAATTC
28130 AGCTCAA-TC
1 AGCTCAATTC
*
28139 GAGCTCAATTT
1 -AGCTCAATTC
28150 AGCTACAATTC
1 AGCT-CAATTC
28161 AGCTCA
1 AGCTCA
28167 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:29555 original size:12 final size:11
Alignment explanation
Indices: 29529--29561 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
29519 ATTGGAGTAA
29529 CAAAAAAAA-T
1 CAAAAAAAATT
29539 CAAAAAAAATT
1 CAAAAAAAATT
29550 CGAAAAAAAATT
1 C-AAAAAAAATT
29562 GATTGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
11 2 0.10
12 10 0.48
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:29556 original size:13 final size:12
Alignment explanation
Indices: 29540--29600 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 12
29530 AAAAAAAATC
29540 AAAAAAAATTCGA
1 AAAAAAAATT-GA
29553 AAAAAAATTGATTGAA
1 AAAAAAA---ATTG-A
*
29569 AAAAAAAATTCA
1 AAAAAAAATTGA
*
29581 AAAAAATAAGTGA
1 AAAAAA-AATTGA
29594 AAAAAAA
1 AAAAAAA
29601 TCGAGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
12 8 0.20
13 20 0.50
15 1 0.03
16 11 0.28
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:29583 original size:27 final size:27
Alignment explanation
Indices: 29540--29600 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 27
29530 AAAAAAAATC
* *
29540 AAAAAAAATTCGAAAAAAAATTGATTGAA
1 AAAAAAAATTC-AAAAAAAA-TAAGTGAA
29569 AAAAAAAATTC-AAAAAAATAAGTGAA
1 AAAAAAAATTCAAAAAAAATAAGTGAA
29595 AAAAAA
1 AAAAAA
29601 TCGAGCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 12 0.40
27 7 0.23
29 11 0.37
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.16
Consensus pattern (27 bp):
AAAAAAAATTCAAAAAAAATAAGTGAA
Found at i:29649 original size:29 final size:26
Alignment explanation
Indices: 29579--29652 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
29569 AAAAAAAATT
*
29579 CAAAAAAATAAGTGAAAAAAAATCGAG
1 CAAAAAAA-AAGTGAAAAAAAATCAAG
*
29606 CAAAAAAAAGGGTGACCAAAAAAATCAAG
1 CAAAAAAAA-AGTGA--AAAAAAATCAAG
*
29635 TTAAAAAAAAAGTGAAAA
1 -CAAAAAAAAAGTGAAAA
29653 GTCTTGCGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 1 0.03
27 15 0.38
29 15 0.38
30 8 0.21
ACGTcount: A:0.66, C:0.08, G:0.15, T:0.11
Consensus pattern (26 bp):
CAAAAAAAAAGTGAAAAAAAATCAAG
Found at i:30616 original size:18 final size:18
Alignment explanation
Indices: 30578--30616 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
30568 AAATCGAAAG
* **
30578 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
30596 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
30614 AAA
1 AAA
30617 GAGAGTGAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.08
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:32328 original size:10 final size:10
Alignment explanation
Indices: 32313--32350 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
32303 GCTCGTTTCC
*
32313 AGCTCACTCG
1 AGCTCAATCG
32323 AGCTCAAGTC-
1 AGCTCAA-TCG
32333 AGCTCAATCG
1 AGCTCAATCG
32343 AGCTCAAT
1 AGCTCAAT
32351 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:32337 original size:20 final size:20
Alignment explanation
Indices: 32312--32349 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
32302 AGCTCGTTTC
*
32312 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
32332 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
32350 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:32356 original size:20 final size:20
Alignment explanation
Indices: 32313--32373 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
32303 GCTCGTTTCC
* * *
32313 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
32333 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
32353 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
32373 A
1 A
32374 TTTCATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:32367 original size:11 final size:10
Alignment explanation
Indices: 32323--32369 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
32313 AGCTCACTCG
*
32323 AGCTCAAGTC
1 AGCTCAATTC
32333 AGCTCAA-TC
1 AGCTCAATTC
*
32342 GAGCTCAATTT
1 -AGCTCAATTC
32353 AGCTACAATTC
1 AGCT-CAATTC
32364 AGCTCA
1 AGCTCA
32370 TTTATTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:34525 original size:13 final size:13
Alignment explanation
Indices: 34507--34531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34497 TGGTCATCAT
34507 GGTGTGAACACAA
1 GGTGTGAACACAA
34520 GGTGTGAACACA
1 GGTGTGAACACA
34532 TGATCAATAC
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:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:36309 original size:56 final size:55
Alignment explanation
Indices: 36193--36310 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
36183 TGCATGCTTT
* * * *
36193 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
36247 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
36303 CATTAAAT
1 CATTAAAT
36311 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:36959 original size:20 final size:20
Alignment explanation
Indices: 36934--36988 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
36924 ACGAGTTAAA
* *
36934 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
36954 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
36974 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
36989 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:41390 original size:30 final size:29
Alignment explanation
Indices: 41356--41452 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
41346 TAAACTAAAA
*
41356 TGAGCTAAGTTTTAGCTCGTGAGCTAAGGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAA-GT
* * * * * *
41386 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCT-AAGT
*
41416 TGAGCTAAGGTTTAGCTCGTGAGCTAAAT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAGT
41445 ATGAGCTA
1 -TGAGCTA
41453 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 3 0.06
30 46 0.90
31 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (29 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAGT
Found at i:43646 original size:12 final size:12
Alignment explanation
Indices: 43631--43661 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
43621 TTCTTTTTGC
43631 TTTTCAAAGGCT
1 TTTTCAAAGGCT
43643 TTTTCAAAGGCT
1 TTTTCAAAGGCT
43655 TTTTCAA
1 TTTTCAA
43662 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:43751 original size:36 final size:36
Alignment explanation
Indices: 43710--43780 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
43700 TCTTGCCTCT
43710 CTTTTCTTTTT-ATTTCTTTTTCTTT-TTCTTCTCTTG
1 CTTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTG
*
43746 CTTTTCTTTTTCCTTTCTTTTCTTTGTTTTCTCTT
1 CTTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
43781 TACAAGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 26 0.81
37 6 0.19
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75
Consensus pattern (36 bp):
CTTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTG
Found at i:43752 original size:20 final size:19
Alignment explanation
Indices: 43709--43780 Score: 68
Period size: 16 Copynumber: 4.1 Consensus size: 19
43699 CTCTTGCCTC
*
43709 TCTTTTCTTTTTATT-TC-
1 TCTTTTCTTTTTCTTCTCT
43726 T-TTTTCTTTTTCTTCTCT
1 TCTTTTCTTTTTCTTCTCT
43744 TGCTTTTCTTTTTC--CT-T
1 T-CTTTTCTTTTTCTTCTCT
43761 TCTTTTCTTTGTT-TTCTCT
1 TCTTTTCTTT-TTCTTCTCT
43780 T
1 T
43781 TACAAGAATG
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
16 21 0.46
17 7 0.15
18 5 0.11
19 2 0.04
20 11 0.24
ACGTcount: A:0.01, C:0.21, G:0.03, T:0.75
Consensus pattern (19 bp):
TCTTTTCTTTTTCTTCTCT
Found at i:43762 original size:11 final size:11
Alignment explanation
Indices: 43709--43770 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 11
43699 CTCTTGCCTC
43709 TCTTTTCTTTT
1 TCTTTTCTTTT
*
43720 T-ATTTCTTTT
1 TCTTTTCTTTT
43730 TCTTTTTCTTCTCT
1 TC-TTTTCTT-T-T
43744 TGCTTTTCTTTT
1 T-CTTTTCTTTT
*
43756 TCCTTTC-TTT
1 TCTTTTCTTTT
43766 TCTTT
1 TCTTT
43771 GTTTTCTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 16 0.38
11 6 0.14
12 8 0.19
13 2 0.05
14 9 0.21
15 1 0.02
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.76
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:43762 original size:25 final size:26
Alignment explanation
Indices: 43722--43777 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
43712 TTTCTTTTTA
*
43722 TTTCTTTTTCTTTTTCTTCTC-TTGCT
1 TTTCTTTTTCTCTTTCTTCTCTTTG-T
*
43748 TTTCTTTTTC-CTTTCTTTTCTTTGT
1 TTTCTTTTTCTCTTTCTTCTCTTTGT
43773 TTTCT
1 TTTCT
43778 CTTTACAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.00, C:0.21, G:0.04, T:0.75
Consensus pattern (26 bp):
TTTCTTTTTCTCTTTCTTCTCTTTGT
Found at i:46897 original size:37 final size:37
Alignment explanation
Indices: 46846--46916 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
46836 CATTCTTGTA
46846 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
46883 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
46917 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:46916 original size:6 final size:6
Alignment explanation
Indices: 46856--46905 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
46846 AAGAGAAAAC
*
46856 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
46905 A
1 A
46906 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:46998 original size:11 final size:12
Alignment explanation
Indices: 46966--46996 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
46956 TTGAGAGAAC
46966 TTGAAAAAGCCT
1 TTGAAAAAGCCT
46978 TTGAAAAAGCCT
1 TTGAAAAAGCCT
46990 TTGAAAA
1 TTGAAAA
46997 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:50237 original size:7 final size:7
Alignment explanation
Indices: 50225--50254 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
50215 ATTTGTAAAG
50225 GACTTTT
1 GACTTTT
50232 GACTTTT
1 GACTTTT
50239 GACTTTT
1 GACTTTT
50246 GACTTTT
1 GACTTTT
50253 GA
1 GA
50255 TCATTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (7 bp):
GACTTTT
Found at i:51574 original size:22 final size:22
Alignment explanation
Indices: 51549--51593 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
51539 TTTTTTTAAC
51549 TCGATTTTTTTTGAATTTTTTT
1 TCGATTTTTTTTGAATTTTTTT
**
51571 TCGATTTTTTTTTCATTTTTTT
1 TCGATTTTTTTTGAATTTTTTT
51593 T
1 T
51594 TTCAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.07, G:0.07, T:0.76
Consensus pattern (22 bp):
TCGATTTTTTTTGAATTTTTTT
Found at i:51597 original size:12 final size:11
Alignment explanation
Indices: 51553--51594 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
51543 TTTAACTCGA
* *
51553 TTTTTTTTGAA
1 TTTTTTTTCAT
51564 TTTTTTTTCGAT
1 TTTTTTTTC-AT
51576 TTTTTTTTCAT
1 TTTTTTTTCAT
51587 TTTTTTTT
1 TTTTTTTT
51595 TCAAATTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.81
Consensus pattern (11 bp):
TTTTTTTTCAT
Found at i:51602 original size:14 final size:12
Alignment explanation
Indices: 51564--51597 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
51554 TTTTTTTGAA
51564 TTTTTTTTCGA-T
1 TTTTTTTTC-ATT
51576 TTTTTTTTCATT
1 TTTTTTTTCATT
51588 TTTTTTTTCA
1 TTTTTTTTCA
51598 AATTTCCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 1 0.05
12 20 0.95
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTTTTTCATT
Found at i:53317 original size:30 final size:30
Alignment explanation
Indices: 53283--53379 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
53273 TAAACTAAAA
*
53283 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * * *
53313 TGAGCTGAGGCTAAACTCCTAAGGTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
53343 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
53372 ATGAGCTA
1 -TGAGCTA
53380 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:55952 original size:43 final size:43
Alignment explanation
Indices: 55902--55988 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
55892 ATTTGTGATT
** *
55902 TCGATATGTGTTTACGTGTAAGAACC-TGTCTGGGACAGTGGCA
1 TCGATATGTGGCTACATGTAAG-ACCATGTCTGGGACAGTGGCA
*
55945 TCGATATGTGGCTACATGTAAGACCATGTCTGGGACATTGGCA
1 TCGATATGTGGCTACATGTAAGACCATGTCTGGGACAGTGGCA
55988 T
1 T
55989 TGTATGAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 3 0.08
43 36 0.92
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
TCGATATGTGGCTACATGTAAGACCATGTCTGGGACAGTGGCA
Found at i:67475 original size:16 final size:16
Alignment explanation
Indices: 67451--67482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
67441 CTTTGTGTAT
*
67451 TCAGTATTAAAAAAAA
1 TCAGAATTAAAAAAAA
67467 TCAGAATTAAAAAAAA
1 TCAGAATTAAAAAAAA
67483 AGAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (16 bp):
TCAGAATTAAAAAAAA
Done.