Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1393
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: 57121
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:571 original size:19 final size:19
Alignment explanation
Indices: 547--599 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
537 CACAAAAAAA
547 TTTTCT-TTATCTTTCTTT
1 TTTTCTCTTATCTTTCTTT
* *
565 CTTTTCTCTTTTTTTTCTTT
1 -TTTTCTCTTATCTTTCTTT
*
585 TTTTCTCTTTTCTTT
1 TTTTCTCTTATCTTT
600 TCTTCCTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTCTCTTATCTTTCTTT
Found at i:583 original size:20 final size:20
Alignment explanation
Indices: 558--603 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
548 TTTCTTTATC
558 TTTCTTTCTTTTCTCTTTT-T
1 TTTCTTT-TTTTCTCTTTTCT
578 TTTCTTTTTTTCTCTTTTCT
1 TTTCTTTTTTTCTCTTTTCT
598 TTTCTT
1 TTTCTT
604 CCTTCTCTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTTTCTCTTTTCT
Found at i:584 original size:24 final size:26
Alignment explanation
Indices: 547--603 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
537 CACAAAAAAA
547 TTTTCTTTATCTTTCTTTCT-TTTCTC
1 TTTTCTTTATCTTTCTTTCTCTTT-TC
*
573 TTTT-TTT-TCTTTTTTTCTCTTTTC
1 TTTTCTTTATCTTTCTTTCTCTTTTC
597 TTTTCTT
1 TTTTCTT
604 CCTTCTCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 16 0.57
25 8 0.29
26 4 0.14
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTCTTTATCTTTCTTTCTCTTTTC
Found at i:603 original size:10 final size:10
Alignment explanation
Indices: 547--603 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
537 CACAAAAAAA
547 TTTTCTTTATC
1 TTTTCTTT-TC
558 -TTTC-TTTC
1 TTTTCTTTTC
*
566 TTTTCTCTTTT
1 TTTTCT-TTTC
577 TTTTCTTTT-
1 TTTTCTTTTC
586 TTTCTCTTTTC
1 TTT-TCTTTTC
597 TTTTCTT
1 TTTTCTT
604 CCTTCTCTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
8 2 0.05
9 9 0.22
10 17 0.43
11 12 0.30
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTC
Found at i:609 original size:19 final size:19
Alignment explanation
Indices: 558--611 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
548 TTTCTTTATC
*
558 TTTCTTTCTTTTCTCTTTTT
1 TTTCTTTC-CTTCTCTTTTT
**
578 TTTCTTTTTTTCTCTTTTCT
1 TTTCTTTCCTTCTCTTTT-T
598 TTTC-TTCCTTCTCT
1 TTTCTTTCCTTCTCT
612 CCCTTCATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTCTTTCCTTCTCTTTTT
Found at i:1159 original size:15 final size:15
Alignment explanation
Indices: 1135--1183 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1125 ATAAAATAAA
*
1135 ATAAATTATTAATAT
1 ATAAAATATTAATAT
*
1150 ATAAAATATTTATAT
1 ATAAAATATTAATAT
1165 A-AAAATA-TAATATT
1 ATAAAATATTAATA-T
1179 ATAAA
1 ATAAA
1184 TAAAAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAATATTAATAT
Found at i:1285 original size:2 final size:2
Alignment explanation
Indices: 1278--1302 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1268 GAATGTAAAA
1278 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1303 CCACGTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2594 original size:33 final size:32
Alignment explanation
Indices: 2535--2599 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
2525 TTTGAGTCAA
2535 TGTATCGATACAATTCTTCATATATCGATACAT
1 TGTATCGATACAATTC-TCATATATCGATACAT
*
2568 TGTATCGATACAATGTGC-CATGTATCGATACA
1 TGTATCGATACAAT-T-CTCATATATCGATACA
2600 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAATTCTCATATATCGATACAT
Found at i:2652 original size:20 final size:20
Alignment explanation
Indices: 2627--2679 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2617 TACTGCCAAT
*
2627 TTCATGTATTGATACCTTTG
1 TTCATGTATTGATACATTTG
2647 TTCATGTATTGATACATTTG
1 TTCATGTATTGATACATTTG
* *
2667 -ACATGTATCGATA
1 TTCATGTATTGATA
2680 TAATGTATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (20 bp):
TTCATGTATTGATACATTTG
Found at i:2673 original size:19 final size:19
Alignment explanation
Indices: 2629--2711 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
2619 CTGCCAATTT
* *
2629 CATGTATTGATACCTTTGTT
1 CATGTATTGATACATTTG-A
2649 CATGTATTGATACATTTGA
1 CATGTATTGATACATTTGA
*
2668 CATGTATCGAT--A--T-A
1 CATGTATTGATACATTTGA
*
2682 -ATGTATCGATACATTTGA
1 CATGTATTGATACATTTGA
2700 CATGTATTGATA
1 CATGTATTGATA
2712 TAATGTATCG
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
13 10 0.19
14 1 0.02
15 2 0.04
17 2 0.04
18 1 0.02
19 20 0.38
20 17 0.32
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (19 bp):
CATGTATTGATACATTTGA
Found at i:2686 original size:32 final size:32
Alignment explanation
Indices: 2650--2726 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
2640 ACCTTTGTTC
*
2650 ATGTATTGATACATTTGACATGTATCGATATA
1 ATGTATCGATACATTTGACATGTATCGATATA
*
2682 ATGTATCGATACATTTGACATGTATTGATATA
1 ATGTATCGATACATTTGACATGTATCGATATA
2714 ATGTATCGATACA
1 ATGTATCGATACA
2727 AAGCATAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (32 bp):
ATGTATCGATACATTTGACATGTATCGATATA
Found at i:9273 original size:10 final size:10
Alignment explanation
Indices: 9258--9284 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9248 TGCTAACTAA
9258 GTTTTTGTTT
1 GTTTTTGTTT
9268 GTTTTTGTTT
1 GTTTTTGTTT
9278 GTTTTTG
1 GTTTTTG
9285 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:18978 original size:1 final size:1
Alignment explanation
Indices: 18972--19095 Score: 68
Period size: 1 Copynumber: 124.0 Consensus size: 1
18962 GGCGTCCTCC
* * * ** ** * * *
18972 AAAAAAACAAAAAAAAAAACAAAACAAAAAAAAACGAAAAAATGAAAAAACAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** ** * * * *
19037 CAAAACAAAAAAAACGAAAAAAATGAAAAAACAAAAAAAAACAAAACAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19096 GAGGGTCCGG
Statistics
Matches: 87, Mismatches: 36, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 87 1.00
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:18987 original size:10 final size:10
Alignment explanation
Indices: 18972--19095 Score: 98
Period size: 10 Copynumber: 12.5 Consensus size: 10
18962 GGCGTCCTCC
18972 AAAAAAAC--
1 AAAAAAACAA
18980 AAAAAAA-AA
1 AAAAAAACAA
*
18989 AACAAAACAA
1 AAAAAAACAA
18999 AAAAAAACGAA
1 AAAAAAAC-AA
*
19010 AAAATGAA-AA
1 AAAA-AAACAA
*
19020 AACAAAACAA
1 AAAAAAACAA
*
19030 AACAAAACAA
1 AAAAAAACAA
19040 AACAAAAA-AA
1 AA-AAAAACAA
*
19050 ACGAAAAAA-AT
1 A--AAAAAACAA
*
19061 GAAAAAACAA
1 AAAAAAACAA
19071 AAAAAAACAA
1 AAAAAAACAA
*
19081 AACAAAACAA
1 AAAAAAACAA
19091 AAAAA
1 AAAAA
19096 GAGGGTCCGG
Statistics
Matches: 94, Mismatches: 12, Indels: 18
0.76 0.10 0.15
Matches are distributed among these distances:
8 7 0.07
9 14 0.15
10 54 0.57
11 16 0.17
12 3 0.03
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.02
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:19012 original size:36 final size:36
Alignment explanation
Indices: 18972--19095 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
18962 GGCGTCCTCC
*
18972 AAAAAAACAAAAAAAAAAACAAAACAAAAAAAAACG
1 AAAAAAACAAAAAAAAAAACAAAACAAAAAAAAACA
** * *
19008 AAAAAATGAAAAAACAAAACAAAACAAAACAAAACA
1 AAAAAAACAAAAAAAAAAACAAAACAAAAAAAAACA
**
19044 AAAAAAACGAAAAAAATGAA-AAAACAAAAAAAAACA
1 AAAAAAAC-AAAAAAAAAAACAAAACAAAAAAAAACA
19080 AAACAAAACAAAAAAA
1 AAA-AAAACAAAAAAA
19096 GAGGGTCCGG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
36 62 0.83
37 13 0.17
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.02
Consensus pattern (36 bp):
AAAAAAACAAAAAAAAAAACAAAACAAAAAAAAACA
Found at i:19043 original size:46 final size:46
Alignment explanation
Indices: 18973--19095 Score: 200
Period size: 46 Copynumber: 2.7 Consensus size: 46
18963 GCGTCCTCCA
18973 AAAAAAC-AAAAAAA-AAAACAAAACAAAAAAAAACG-AAAAAATG
1 AAAAAACAAAAAAAACAAAACAAAACAAAAAAAAACGAAAAAAATG
19016 AAAAAACAAAACAAAACAAAACAAAAC-AAAAAAAACGAAAAAAATG
1 AAAAAACAAAA-AAAACAAAACAAAACAAAAAAAAACGAAAAAAATG
19062 AAAAAACAAAAAAAAACAAAACAAAACAAAAAAA
1 AAAAAAC-AAAAAAAACAAAACAAAACAAAAAAA
19096 GAGGGTCCGG
Statistics
Matches: 74, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
43 7 0.09
44 3 0.04
45 14 0.19
46 40 0.54
47 10 0.14
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.02
Consensus pattern (46 bp):
AAAAAACAAAAAAAACAAAACAAAACAAAAAAAAACGAAAAAAATG
Found at i:20604 original size:30 final size:29
Alignment explanation
Indices: 20535--20858 Score: 322
Period size: 30 Copynumber: 11.1 Consensus size: 29
20525 TTTATCACCC
*
20535 TTCAAAAGTCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
*
20565 TTC-AAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
**
20594 TTCAAAAGCCCACAAGTCAGTGGCAA-CC
1 TTCAAAAGCCCACAAGTCAGTGGCAATTT
* *
20622 TTC-AAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA--ATTT
**
20652 TTCAAAAGCCCACAAGTCAGTGGCAACAT
1 TTCAAAAGCCCACAAGTCAGTGGCAATTT
* **
20681 TT-AAAAGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
20710 TTCAAAAGCCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
**
20740 TTCAAAAGCCCACAAGTCAGTGGCAACCT
1 TTCAAAAGCCCACAAGTCAGTGGCAATTT
* **
20769 TT-AAAAGTCCACAAGTCAGTGGCAA-CC
1 TTCAAAAGCCCACAAGTCAGTGGCAATTT
* * *
20796 TTC-AAAGCCCACAAATTAGTGGCACCTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA--ATTT
* *
20826 TTC-GAAGCCCACAAGTCAGTGGCACCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-ATTT
20855 TTCA
1 TTCA
20859 TCTTTAAGTC
Statistics
Matches: 248, Mismatches: 34, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
27 41 0.17
28 46 0.19
29 45 0.18
30 96 0.39
31 20 0.08
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (29 bp):
TTCAAAAGCCCACAAGTCAGTGGCAATTT
Found at i:20671 original size:58 final size:58
Alignment explanation
Indices: 20535--20853 Score: 382
Period size: 58 Copynumber: 5.5 Consensus size: 58
20525 TTTATCACCC
* ** **
20535 TTCAAAAGTCCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTCAGTGGCA-TTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-A-CCTTCAAAGCCCACAAGTCAGTGGCACCCTTT
*
20594 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCACCCTTT
* * *
20652 TTCAAAAGCCCACAAGTCAGTGGCAACATTTAAAAGCCCACAAGTTAGTGGCACCC-TT
1 TTCAAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAGCCCACAAGTCAGTGGCACCCTTT
** *
20710 TTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCACAAGTCAGTGGCAACC--T
1 TTCAAAAGCCCACAAGTCAGTGGCA-A-CCTTC-AAAGCCCACAAGTCAGTGGCACCCTTT
* * * *
20769 TT-AAAAGTCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAATTAGTGGCACCTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCACCCTTT
*
20826 TTC-GAAGCCCACAAGTCAGTGGC-ACCTT
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTT
20854 TTTCATCTTT
Statistics
Matches: 229, Mismatches: 23, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
55 20 0.09
56 8 0.03
57 45 0.20
58 79 0.34
59 55 0.24
60 22 0.10
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (58 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACAAGTCAGTGGCACCCTTT
Found at i:20741 original size:88 final size:85
Alignment explanation
Indices: 20533--20849 Score: 406
Period size: 88 Copynumber: 3.7 Consensus size: 85
20523 CATTTATCAC
* * ***
20533 CCTTCAAAAGTCCACAAGTCAGTGGCA-TATTTTTCAAAGCCCACAAGTCAGTGGCATTTTTTTC
1 CCTTC-AAAGCCCACAAATCAGTGGCACTATTTTTCAAAGCCCACAAGTCAGTGGCA-ACATTT-
20597 AAAAGCCCACAAGTCAGTGGCAA
63 AAAAGCCCACAAGTCAGTGGCAA
**
20620 CCTTCAAAGCCCACAAATCAGTGGCACCCTTTTTCAAAAGCCCACAAGTCAGTGGCAACATTTAA
1 CCTTCAAAGCCCACAAATCAGTGGCACTATTTTTC-AAAGCCCACAAGTCAGTGGCAACATTTAA
* *
20685 AAGCCCACAAGTTAGTGGCAC
65 AAGCCCACAAGTCAGTGGCAA
* *
20706 CCTTTTCAAAAGCCCACAAGTCAGTGGCA-TATTTTTCAAAAGCCCACAAGTCAGTGGCAACCTT
1 CC--TTC-AAAGCCCACAAATCAGTGGCACTATTTTTC-AAAGCCCACAAGTCAGTGGCAACATT
*
20770 TAAAAGTCCACAAGTCAGTGGCAA
62 TAAAAGCCCACAAGTCAGTGGCAA
* *
20794 CCTTCAAAGCCCACAAATTAGTGGCACCT-TTTTTCGAAGCCCACAAGTCAGTGGCA
1 CCTTCAAAGCCCACAAATCAGTGGCA-CTATTTTTCAAAGCCCACAAGTCAGTGGCA
20850 CCTTTTTCAT
Statistics
Matches: 204, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
85 39 0.19
86 51 0.25
87 15 0.07
88 79 0.39
89 20 0.10
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (85 bp):
CCTTCAAAGCCCACAAATCAGTGGCACTATTTTTCAAAGCCCACAAGTCAGTGGCAACATTTAAA
AGCCCACAAGTCAGTGGCAA
Found at i:20921 original size:43 final size:43
Alignment explanation
Indices: 20860--20949 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
20850 CCTTTTTCAT
*
20860 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
* *
20903 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
20946 CTTT
1 CTTT
20950 TCCATCTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
Found at i:20981 original size:52 final size:53
Alignment explanation
Indices: 20903--21056 Score: 184
Period size: 52 Copynumber: 2.9 Consensus size: 53
20893 ACATTGGCAC
*
20903 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAG
* * * *
20955 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAG
* * * * * *
21010 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
21057 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 6 0.07
55 35 0.42
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAG
Found at i:21726 original size:52 final size:52
Alignment explanation
Indices: 21648--21808 Score: 295
Period size: 52 Copynumber: 3.1 Consensus size: 52
21638 TGTGGGGACG
21648 AATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACATGCAGGCA
1 AATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACATGCAGGCA
21700 AATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACATGCAGGCA
1 AATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACATGCAGGCA
** *
21752 AATTTGCCCAGATGTATCGATACACTATTCAATGTATCGATACATGCAGGTA
1 AATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACATGCAGGCA
21804 AATTT
1 AATTT
21809 TCATATTTCG
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 106 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
AATTTGCCCAGATGTATCGATACACTATAAAATGTATCGATACATGCAGGCA
Found at i:28216 original size:13 final size:13
Alignment explanation
Indices: 28198--28223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28188 CAATTTGGTC
28198 ATGTATCGATACA
1 ATGTATCGATACA
28211 ATGTATCGATACA
1 ATGTATCGATACA
28224 TCTTGTATGT
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:28223 original size:34 final size:32
Alignment explanation
Indices: 28175--28243 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
28165 CGTTACAAGC
28175 CAATGTATCAATACAAT-TTGGTCATGTATCGATA
1 CAATGTATCAATAC-ATCTT-GT-ATGTATCGATA
*
28209 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCAATACATCTTGTATGTATCGATA
28241 CAA
1 CAA
28244 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 14 0.42
33 4 0.12
34 15 0.45
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (32 bp):
CAATGTATCAATACATCTTGTATGTATCGATA
Found at i:28942 original size:17 final size:17
Alignment explanation
Indices: 28922--28956 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28912 AATAAAACAA
28922 TTTCCTTTAATCACATG
1 TTTCCTTTAATCACATG
28939 TTTCCTTTAATCACATG
1 TTTCCTTTAATCACATG
28956 T
1 T
28957 ATCTTTCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (17 bp):
TTTCCTTTAATCACATG
Found at i:30351 original size:20 final size:21
Alignment explanation
Indices: 30322--30363 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
30312 TGGAGGCTGC
30322 CCGGTCGCGACCTGG-GAGTG
1 CCGGTCGCGACCTGGTGAGTG
*
30342 CCGGTTGCGACCTGGTGAGTG
1 CCGGTCGCGACCTGGTGAGTG
30363 C
1 C
30364 TGGCTAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.10, C:0.29, G:0.43, T:0.19
Consensus pattern (21 bp):
CCGGTCGCGACCTGGTGAGTG
Found at i:30830 original size:13 final size:13
Alignment explanation
Indices: 30797--30833 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
30787 TATAATTGCC
*
30797 ATGTATCAATACA
1 ATGTATCGATACA
*
30810 GTGTATCGATACA
1 ATGTATCGATACA
30823 ATGTATCGATA
1 ATGTATCGATA
30834 TAGAGAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:35862 original size:16 final size:16
Alignment explanation
Indices: 35841--35871 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35831 ATCCCAATTG
35841 CTTCAATTAATCTTTC
1 CTTCAATTAATCTTTC
35857 CTTCAATTAATCTTT
1 CTTCAATTAATCTTT
35872 ACTTGTATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (16 bp):
CTTCAATTAATCTTTC
Found at i:38929 original size:12 final size:13
Alignment explanation
Indices: 38906--38937 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
38896 AAATTTAAAC
38906 AAAATATTTTATT
1 AAAATATTTTATT
38919 AAAAT-TTTTATT
1 AAAATATTTTATT
38931 AAAATAT
1 AAAATAT
38938 AAAAATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAAATATTTTATT
Found at i:41125 original size:18 final size:18
Alignment explanation
Indices: 41085--41119 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41075 CTTATCATAT
*
41085 TCATCTTCTTCATCTTCA
1 TCATCTTCTTCAACTTCA
*
41103 TCATCTTCTTTAACTTC
1 TCATCTTCTTCAACTTC
41120 TGCATCGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.51
Consensus pattern (18 bp):
TCATCTTCTTCAACTTCA
Found at i:45985 original size:20 final size:20
Alignment explanation
Indices: 45954--45994 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
45944 TAATATATAT
*
45954 ATATATATATATATTCTATAAA
1 ATATACATAT-TATT-TATAAA
45976 ATATACATATTATTTATAA
1 ATATACATATTATTTATAA
45995 TAGTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATACATATTATTTATAAA
Found at i:48588 original size:103 final size:102
Alignment explanation
Indices: 48398--48618 Score: 291
Period size: 103 Copynumber: 2.1 Consensus size: 102
48388 TTTATTCATG
* * * * *
48398 GGGATACTCCAACCCTAACCTTTTGAAGGGATACTTTAACCACGCTCTTCAAAATTTATCTAGAT
1 GGGATACTCCAACCCTAACCTTTCGAAAGGATACTTCAACCACGCTCTTCAAAATTTATCAACAT
*
48463 TTAAACTCCTCCTTTGTCAAAATTATTTGTTATCCAC
66 TTAAACTCCTCCTTTATCAAAATTATTTGTTATCCAC
* * *
48500 AGGGATACTCCAA-CCTCGACCTTTCGAAAGGATACTTCAGCCCCGCTCTTCAAAATTTATCAAC
1 -GGGATACTCCAACCCT-AACCTTTCGAAAGGATACTTCAACCACGCTCTTCAAAATTTATCAAC
* * * *
48564 ATTTGAACTCTTCTTTTATTAAAATTATTTGTTATCCAC
64 ATTTAAACTCCTCCTTTATCAAAATTATTTGTTATCCAC
48603 GTGGATACTCCAACCC
1 G-GGATACTCCAACCC
48619 CATCTTCAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
102 4 0.04
103 96 0.94
104 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (102 bp):
GGGATACTCCAACCCTAACCTTTCGAAAGGATACTTCAACCACGCTCTTCAAAATTTATCAACAT
TTAAACTCCTCCTTTATCAAAATTATTTGTTATCCAC
Found at i:50105 original size:20 final size:22
Alignment explanation
Indices: 50063--50105 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
50053 ATTTAATCGG
* *
50063 TTTATTTTTAAAATATAATTAA
1 TTTATTTTTAAAATAAAAATAA
50085 TTTA-TTTT-AAATAAAAATAA
1 TTTATTTTTAAAATAAAAATAA
50105 T
1 T
50106 ATAATACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTATTTTTAAAATAAAAATAA
Found at i:55657 original size:32 final size:32
Alignment explanation
Indices: 55616--55679 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
55606 TATTACAAGC
55616 TAATGTATCGATACAT-TTGGGATGTATCGATA
1 TAATGTATCGATACATCTTGGG-TGTATCGATA
*
55648 TAATGTATCGATACATCTTGTGTGTATCGATA
1 TAATGTATCGATACATCTTGGGTGTATCGATA
55680 CAAACAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (32 bp):
TAATGTATCGATACATCTTGGGTGTATCGATA
Found at i:55782 original size:13 final size:13
Alignment explanation
Indices: 55764--55788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55754 CATTTGGTCG
55764 TGTATCGATACAA
1 TGTATCGATACAA
55777 TGTATCGATACA
1 TGTATCGATACA
55789 TTTGAAGGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:55826 original size:20 final size:20
Alignment explanation
Indices: 55777--55826 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
55767 ATCGATACAA
55777 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTTGAAGG
**
55797 TG-GGCGATACATTTGAAGG
1 TGTATCGATACATTTGAAGG
55816 TGTATCGATAC
1 TGTATCGATAC
55827 TTTTCAGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATTTGAAGG
Found at i:56382 original size:22 final size:23
Alignment explanation
Indices: 56343--56388 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
56333 TTTTCTTTTC
56343 TCTCCCCCTTAATCAAAAAAATT
1 TCTCCCCCTTAATCAAAAAAATT
*
56366 TCTCCCCCTTAAT-AAAATAATT
1 TCTCCCCCTTAATCAAAAAAATT
56388 T
1 T
56389 AACAATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (23 bp):
TCTCCCCCTTAATCAAAAAAATT
Done.