Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold255
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: 37177
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:2358 original size:12 final size:13
Alignment explanation
Indices: 2336--2372 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2326 TGGGATATGC
*
2336 AATGAATGAATTG
1 AATGCATGAATTG
2349 -ATGCATGAA-TG
1 AATGCATGAATTG
2360 AATGCATGAATTG
1 AATGCATGAATTG
2373 TCAAATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (13 bp):
AATGCATGAATTG
Found at i:5795 original size:21 final size:20
Alignment explanation
Indices: 5743--5796 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
5733 AATTTTGAAG
5743 CACGAAATTTTTTTTAAAAA
1 CACGAAATTTTTTTTAAAAA
* * *
5763 AATGAAAGTTTTTTTTTAAAA
1 CACGAAA-TTTTTTTTAAAAA
5784 CACGAGAATTTTT
1 CACGA-AATTTTT
5797 AAACACGGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 5 0.19
21 20 0.74
22 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (20 bp):
CACGAAATTTTTTTTAAAAA
Found at i:5797 original size:17 final size:17
Alignment explanation
Indices: 5775--6158 Score: 160
Period size: 17 Copynumber: 21.8 Consensus size: 17
5765 TGAAAGTTTT
5775 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAGAA
5792 TTTTT-AAACACG-GAAA
1 TTTTTAAAACACGAG-AA
** *
5808 TTTCAAAAACACGAAAA
1 TTTTTAAAACACGAGAA
* *
5825 TTTTTAAAACACGACATT
1 TTTTTAAAACACGAGA-A
*
5843 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAGAA
* * *
5860 TTTTTAAAACAAGACAT
1 TTTTTAAAACACGAGAA
***
5877 TTTTTAGAAA-ACGATTT
1 TTTTTA-AAACACGAGAA
*
5894 TTTTTAAAATCACCG-GAG
1 TTTTTAAAA-CA-CGAGAA
*
5912 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAGAA
* *
5930 TCTTTGAAACACCGA-AA
1 TTTTTAAAACA-CGAGAA
5947 TTTTTGAAAACACGA-AA
1 TTTTT-AAAACACGAGAA
*
5964 TTTTTTGAAACACGA-AA
1 -TTTTTAAAACACGAGAA
* *
5981 TTTTTTTGAAAATACGAAGAT
1 --TTTTT-AAAACACG-AGAA
**
6002 TTTTTTTAACACG-GAAA
1 TTTTTAAAACACGAG-AA
* *
6019 TTTTTGAAACACG-GTCAT
1 TTTTTAAAACACGAG--AA
*
6037 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAGAA
* **
6055 TTTTTGAAAGACATGA-TT
1 TTTTT-AAA-ACACGAGAA
*
6073 TTTTTGAAAATACG-GAAA
1 TTTTT-AAAACACGAG-AA
* *
6091 TTTATAAAACACGAAAA
1 TTTTTAAAACACGAGAA
* *
6108 TTTTTCTGAAAACAAGAAAA
1 -TTTT-T-AAAACACGAGAA
* *
6128 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAGAA
*
6145 TTTTGAAAACACGA
1 TTTTTAAAACACGA
6159 TTTTTCTTTA
Statistics
Matches: 279, Mismatches: 60, Indels: 56
0.71 0.15 0.14
Matches are distributed among these distances:
15 1 0.00
16 16 0.06
17 128 0.46
18 87 0.31
19 34 0.12
20 12 0.04
21 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:5862 original size:35 final size:34
Alignment explanation
Indices: 5773--6063 Score: 153
Period size: 35 Copynumber: 8.3 Consensus size: 34
5763 AATGAAAGTT
* *
5773 TTTTTTTAAAACACGAGAATTTTT-AAACACGGAA
1 TTTTTTTGAAACACGAAAATTTTTAAAACAC-GAA
* ***
5807 -ATTTCAAAAACACGAAAATTTTTAAAACACGACA
1 TTTTTTTGAAACACGAAAATTTTTAAAACACGA-A
* *
5841 TTTTTTTGAAACACGAGAATTTTTAAAACAAGACA
1 TTTTTTTGAAACACGAAAATTTTTAAAACACGA-A
* *** *
5876 TTTTTTAGAAA-ACGATTTTTTTTAAAATCACCGGA
1 TTTTTTTGAAACACGAAAATTTTTAAAA-CA-CGAA
* * *
5911 -GTTTTTGAAAACACGAAAATCTTTGAAACACCGAA
1 TTTTTTTG-AAACACGAAAATTTTTAAAACA-CGAA
* * *
5946 -ATTTTTGAAAACACGAAATTTTTTGAAACACGAAA
1 TTTTTTTG-AAACACGAAAATTTTTAAAACACG-AA
* * **
5981 TTTTTTTGAAAATACGAAGATTTTTTTTAACACGGAA
1 TTTTTTTG-AAACACGAA-AATTTTTAAAACAC-GAA
* ** *
6018 -ATTTTTGAAACACGGTCATTTTTTGAAAACACGAA
1 TTTTTTTGAAACAC-GAAAATTTTT-AAAACACGAA
**
6053 AATTTTTGAAA
1 TTTTTTTGAAA
6064 GACATGATTT
Statistics
Matches: 206, Mismatches: 37, Indels: 26
0.77 0.14 0.10
Matches are distributed among these distances:
33 21 0.10
34 27 0.13
35 94 0.46
36 49 0.24
37 14 0.07
38 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (34 bp):
TTTTTTTGAAACACGAAAATTTTTAAAACACGAA
Found at i:6023 original size:54 final size:54
Alignment explanation
Indices: 5912--6139 Score: 148
Period size: 54 Copynumber: 4.2 Consensus size: 54
5902 ATCACCGGAG
* * ***
5912 TTTTTGAAAACAC-GAAAATCTTTG-AAACACCG-AAATTTTTGAAAACACGAAAT
1 TTTTTG-AAACACGGAAATTTTTTGAAAACA-CGAAAATTTTTTTTAACACGAAAT
* *
5965 TTTTTGAAACAC-GAAATTTTTTTGAAAATACGAAGATTTTTTTTAACACGGAAA-
1 TTTTTGAAACACGGAAA-TTTTTTGAAAACACGAAAATTTTTTTTAACAC-GAAAT
** *** * *
6019 TTTTTGAAACACGGTCATTTTTTGAAAACACGAAAATTTTTGAAAGACATG-ATT
1 TTTTTGAAACACGGAAATTTTTTGAAAACACGAAAATTTTTTTTA-ACACGAAAT
* * ** * *
6073 TTTTTGAAAATACGGAAA-TTTAT-AAAACACGAAAATTTTTCTGAAAACAAGAAAA
1 TTTTTG-AAACACGGAAATTTTTTGAAAACACGAAAATTTTT-T-TTAACACGAAAT
6128 TTTTTGAAACAC
1 TTTTTGAAACAC
6140 TAGAATTTTG
Statistics
Matches: 139, Mismatches: 25, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
52 10 0.07
53 31 0.22
54 71 0.51
55 27 0.19
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (54 bp):
TTTTTGAAACACGGAAATTTTTTGAAAACACGAAAATTTTTTTTAACACGAAAT
Found at i:6076 original size:36 final size:36
Alignment explanation
Indices: 5932--6139 Score: 167
Period size: 36 Copynumber: 5.8 Consensus size: 36
5922 CACGAAAATC
5932 TTTGAAACACCG-AAATTTTTGAAAACACGAA-A-TTT
1 TTTGAAACA-CGAAAATTTTTG-AAACACGAAGATTTT
* *
5967 TTTGAAACACGAAATTTTTTTGAAAATACGAAGATTTT
1 TTTGAAACACGAAA-ATTTTTG-AAACACGAAGATTTT
* * ***
6005 TTT-TAACACGGAAATTTTTGAAACACGGTCA-TTT
1 TTTGAAACACGAAAATTTTTGAAACACGAAGATTTT
* *
6039 TTTGAAAACACGAAAATTTTTGAAAGAC-ATGATTTT
1 TTTG-AAACACGAAAATTTTTGAAACACGAAGATTTT
* * * * *
6075 TTTGAAAATACGGAAATTTATAAAACACGAAAATTTT
1 TTTG-AAACACGAAAATTTTTGAAACACGAAGATTTT
* *
6112 TCTGAAAACAAGAAAATTTTTGAAACAC
1 TTTG-AAACACGAAAATTTTTGAAACAC
6140 TAGAATTTTG
Statistics
Matches: 138, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
34 8 0.06
35 20 0.14
36 67 0.49
37 37 0.27
38 6 0.04
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (36 bp):
TTTGAAACACGAAAATTTTTGAAACACGAAGATTTT
Found at i:6129 original size:37 final size:35
Alignment explanation
Indices: 5912--6158 Score: 157
Period size: 36 Copynumber: 6.9 Consensus size: 35
5902 ATCACCGGAG
*
5912 TTTTTGAAAACACGAAAA-TCTTTG-AAACACCG-AAA
1 TTTTTG-AAACAC-AAAATTTTTTGAAAACA-CGAAAA
* *
5947 TTTTTGAAAACACGAAATTTTTTG-AAACACGAAATT
1 TTTTTG-AAACACAAAATTTTTTGAAAACACGAAA-A
* * ** *
5983 TTTTTGAAAATACGAAGATTTTTT-TTAACACGGAAA
1 TTTTTG-AAACAC-AAAATTTTTTGAAAACACGAAAA
***
6019 TTTTTGAAACACGGTCATTTTTTGAAAACACGAAAA
1 TTTTTGAAACAC-AAAATTTTTTGAAAACACGAAAA
* * * * *
6055 TTTTTGAAAGACATGATTTTTTTGAAAATACGGAAA
1 TTTTTGAAACACA-AAATTTTTTGAAAACACGAAAA
* * *
6091 TTTATAAAACACGAAAATTTTTCTGAAAACAAGAAAA
1 TTTTTGAAACAC-AAAATTTTT-TGAAAACACGAAAA
*
6128 TTTTTGAAACACTAGAA--TTTTGAAAACACGA
1 TTTTTGAAACAC-AAAATTTTTTGAAAACACGA
6159 TTTTTCTTTA
Statistics
Matches: 167, Mismatches: 36, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
34 15 0.09
35 41 0.25
36 70 0.42
37 41 0.25
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (35 bp):
TTTTTGAAACACAAAATTTTTTGAAAACACGAAAA
Found at i:6750 original size:11 final size:11
Alignment explanation
Indices: 6734--6760 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6724 GTTTTTATTT
6734 TTTTTAATTAC
1 TTTTTAATTAC
6745 TTTTTAATTAC
1 TTTTTAATTAC
6756 TTTTT
1 TTTTT
6761 TTCTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTAATTAC
Found at i:6787 original size:14 final size:14
Alignment explanation
Indices: 6762--6806 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
6752 TTACTTTTTT
6762 TCTTTCTTTTCTTTC
1 TCTTT-TTTTCTTTC
6777 TCTTTTTTTCTTTC
1 TCTTTTTTTCTTTC
*
6791 T-TTTTCTTC-TTC
1 TCTTTTTTTCTTTC
6803 TCTT
1 TCTT
6807 CTTCTTGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 4 0.14
13 9 0.32
14 10 0.36
15 5 0.18
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TCTTTTTTTCTTTC
Found at i:7385 original size:29 final size:30
Alignment explanation
Indices: 7352--7468 Score: 105
Period size: 30 Copynumber: 3.9 Consensus size: 30
7342 TGTAATTTTT
*
7352 AGAAAATTT-AGGATTAAAATGAAATTTAA
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
7381 TGAAAGTTTAAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAAGGGT-TAAAATGAAATTTAA
* *
7411 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * * *
7440 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTAAGGGTTAAAATGAAATTT
7469 TTATTTTTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.16
30 60 0.82
31 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (30 bp):
AGAAAATTTAAGGGTTAAAATGAAATTTAA
Found at i:7407 original size:30 final size:30
Alignment explanation
Indices: 7367--7468 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
7357 ATTTAGGATT
*
7367 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
7397 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
7427 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
7457 AAAATGCAATTT
1 AAAATGAAATTT
7469 TTATTTTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 2 0.03
30 61 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:7484 original size:15 final size:16
Alignment explanation
Indices: 7464--7500 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
7454 GTCAAAATGC
7464 AATTTTTATTTTTT-A
1 AATTTTTATTTTTTGA
*
7479 AATTTTTTTTTTTTGA
1 AATTTTTATTTTTTGA
7495 AATTTT
1 AATTTT
7501 GAAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
AATTTTTATTTTTTGA
Found at i:7491 original size:16 final size:16
Alignment explanation
Indices: 7466--7500 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
7456 CAAAATGCAA
*
7466 TTTTTATTTTTTAAAT
1 TTTTTATTTTTGAAAT
*
7482 TTTTTTTTTTTGAAAT
1 TTTTTATTTTTGAAAT
7498 TTT
1 TTT
7501 GAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTTGAAAT
Found at i:10403 original size:25 final size:25
Alignment explanation
Indices: 10375--10422 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
10365 AGAAACTAGA
10375 TTATTGATATTGATTTTGAAAATAC
1 TTATTGATATTGATTTTGAAAATAC
10400 TTATTGATATTGATTTTGAAAAT
1 TTATTGATATTGATTTTGAAAAT
10423 TGAAGGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (25 bp):
TTATTGATATTGATTTTGAAAATAC
Found at i:12190 original size:22 final size:23
Alignment explanation
Indices: 12165--12213 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
12155 TTTGGTCGTT
*
12165 TAAATAAAAC-ATTTTGGTTTAC
1 TAAATAAAACGATTTTGGTCTAC
*
12187 TAAA-ACAACGATTTTGGTCTAC
1 TAAATAAAACGATTTTGGTCTAC
*
12209 GAAAT
1 TAAAT
12214 TTGAGAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (23 bp):
TAAATAAAACGATTTTGGTCTAC
Found at i:13711 original size:26 final size:26
Alignment explanation
Indices: 13681--13731 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
13671 AAATCAAATA
* *
13681 GTTTAAAATAAATAATATTTAAAAGG
1 GTTTAAAATAAATAACATGTAAAAGG
*
13707 GTTTAAGATAAATAACATGTAAAAG
1 GTTTAAAATAAATAACATGTAAAAG
13732 AGAAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (26 bp):
GTTTAAAATAAATAACATGTAAAAGG
Found at i:14956 original size:14 final size:14
Alignment explanation
Indices: 14937--14967 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14927 TTTGATTGGT
*
14937 GGAAAATATTTTCC
1 GGAAAATATTTTAC
14951 GGAAAATATTTTAC
1 GGAAAATATTTTAC
14965 GGA
1 GGA
14968 TTTTCCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (14 bp):
GGAAAATATTTTAC
Found at i:15464 original size:27 final size:27
Alignment explanation
Indices: 15377--15475 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 27
15367 AAAGGTATAT
15377 TTTCTTGTCCATAGTTTTGTGAATCGG
1 TTTCTTGTCCATAGTTTTGTGAATCGG
* * * *
15404 TTTCTGGGT---TAGTTCCTTTATGTTATTGG
1 TTTCT-TGTCCATAG-T--TTTGTG-AATCGG
15433 TTTCTTGTCCATAGTTTTGTGAATCGG
1 TTTCTTGTCCATAGTTTTGTGAATCGG
15460 TTTCTTGTCCATAGTT
1 TTTCTTGTCCATAGTT
15476 AGAAAGATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 25 0.45
28 14 0.25
29 9 0.16
30 1 0.02
31 3 0.05
ACGTcount: A:0.13, C:0.14, G:0.21, T:0.52
Consensus pattern (27 bp):
TTTCTTGTCCATAGTTTTGTGAATCGG
Found at i:17572 original size:26 final size:26
Alignment explanation
Indices: 17543--17600 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
17533 CATCCTCAAA
17543 CTATAATCTAGATATTAAATTGGTCT
1 CTATAATCTAGATATTAAATTGGTCT
*
17569 CTATAATCTAGATTTTAAATTGGTCT
1 CTATAATCTAGATATTAAATTGGTCT
17595 CTATAA
1 CTATAA
17601 ATTTTGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (26 bp):
CTATAATCTAGATATTAAATTGGTCT
Found at i:17943 original size:14 final size:15
Alignment explanation
Indices: 17921--17997 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
17911 CAATCAAACA
17921 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
17935 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
17950 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
17970 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
17984 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
17998 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:17962 original size:20 final size:20
Alignment explanation
Indices: 17937--17976 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17927 AATATTTTCC
*
17937 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
17957 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
17977 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:17982 original size:34 final size:35
Alignment explanation
Indices: 17925--17991 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
17915 CAAACACCAG
*
17925 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
17960 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
17992 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:17998 original size:14 final size:14
Alignment explanation
Indices: 17960--17999 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
17950 ACAGAAAAGT
*
17960 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
17974 AAATCATTTTACGG
1 AAAACATTTTACAG
17988 AAAACATTTTAC
1 AAAACATTTTAC
18000 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:28135 original size:28 final size:28
Alignment explanation
Indices: 28103--28204 Score: 159
Period size: 28 Copynumber: 3.6 Consensus size: 28
28093 CAAATATGGT
*
28103 ACTTAGTGTACGAAATATTGAGAATGGC
1 ACTTAGTGTACGAAATATTGAGAATGAC
28131 ACTTAGTGTACGAAATATTGAGAATGAC
1 ACTTAGTGTACGAAATATTGAGAATGAC
* *
28159 ACTTAGTGTGCGAGATATTGAGAATGAC
1 ACTTAGTGTACGAAATATTGAGAATGAC
* *
28187 ACTTAGTGTGCAAAATAT
1 ACTTAGTGTACGAAATAT
28205 CGAATGATTC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (28 bp):
ACTTAGTGTACGAAATATTGAGAATGAC
Found at i:31252 original size:20 final size:20
Alignment explanation
Indices: 31222--31266 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
31212 CTGTTTTATT
31222 ATGGG-CCAACTGTATTAAA
1 ATGGGCCCAACTGTATTAAA
* *
31241 ATGGGCCCAACTGTGTTAAT
1 ATGGGCCCAACTGTATTAAA
31261 ATGGGC
1 ATGGGC
31267 AAGACCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTAAA
Found at i:32602 original size:46 final size:45
Alignment explanation
Indices: 32552--32726 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
32542 TGGTTGAGCA
32552 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
32598 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
32645 TCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
32690 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
32727 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 1 0.01
45 24 0.22
46 51 0.47
47 24 0.22
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:32707 original size:92 final size:93
Alignment explanation
Indices: 32549--32718 Score: 297
Period size: 92 Copynumber: 1.8 Consensus size: 93
32539 GGATGGTTGA
* *
32549 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
32614 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
32642 GCATCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
32706 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
32719 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 50 0.68
93 23 0.32
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:35683 original size:15 final size:15
Alignment explanation
Indices: 35663--35720 Score: 89
Period size: 15 Copynumber: 3.7 Consensus size: 15
35653 GTATCTTGGG
35663 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
35678 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
35693 TTTCTTATCTTCTTGGA
1 TTTCTT-TATTC-TGGA
35710 TTTCTTTATTC
1 TTTCTTTATTC
35721 GGTTTCCTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
15 21 0.54
16 8 0.21
17 10 0.26
ACGTcount: A:0.12, C:0.16, G:0.10, T:0.62
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Done.