Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold843
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: 43975
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2141 original size:18 final size:19
Alignment explanation
Indices: 2099--2148 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 19
2089 CAAACAGTAA
*
2099 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
*
2118 TTGTATCGATACGT-AGTG
1 TTGTATCGATACATAAGTG
2136 TTGTATCGATACA
1 TTGTATCGATACA
2149 ATGTCTCGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:5715 original size:34 final size:35
Alignment explanation
Indices: 5652--5718 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
5642 CTAAGTGATT
5652 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
5688 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
5719 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:7412 original size:84 final size:84
Alignment explanation
Indices: 7239--7399 Score: 191
Period size: 84 Copynumber: 1.9 Consensus size: 84
7229 ACTCAAAGAA
* * * * * * *
7239 GAAAATAAATCAATAAGTGTAGAGAATGATTTTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATAAAATAGAGAAGAA
*
7304 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * *
7323 GAAAATAAATCAATGAGTTTAGAAAATAATTCTT-TTAAAAAGAAAATAAATAAAATAGAGGAGA
1 GAAAATAAATCAATAAGTGTAGAAAATAATT-TTCTTAAAAAGAAAATAAATAAAATAGAGAAGA
7387 A-AAGAAATGAGTT
65 ATAAGAAA-GAGTT
7400 GCAAGTGGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
83 5 0.08
84 57 0.89
85 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.17, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATAAAATAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Found at i:10013 original size:13 final size:13
Alignment explanation
Indices: 9995--10019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9985 CATAAAATGT
9995 TGTATCGATACAA
1 TGTATCGATACAA
10008 TGTATCGATACA
1 TGTATCGATACA
10020 TATTTTTTTG
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:10017 original size:33 final size:33
Alignment explanation
Indices: 9975--10044 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
9965 TTCAACGATT
9975 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
10008 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
10041 TGTA
1 TGTA
10045 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:10102 original size:13 final size:13
Alignment explanation
Indices: 10084--10108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10074 ATTACTCACA
10084 TGTATCGATACAT
1 TGTATCGATACAT
10097 TGTATCGATACA
1 TGTATCGATACA
10109 CCGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14271 original size:13 final size:13
Alignment explanation
Indices: 14253--14292 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
14243 TCACTATTCA
*
14253 TGTATCGATACAT
1 TGTATCGATACAC
14266 TGTATCGATACAC
1 TGTATCGATACAC
14279 TGTATCGATACAC
1 TGTATCGATACAC
14292 T
1 T
14293 ATAAATAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:14825 original size:34 final size:35
Alignment explanation
Indices: 14762--14828 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
14752 CTAAATGATT
14762 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
14798 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
14829 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:19377 original size:9 final size:8
Alignment explanation
Indices: 19360--19400 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 8
19350 ACACAAACAA
19360 AAAAAAAC
1 AAAAAAAC
19368 AAACAAAAC
1 AAA-AAAAC
*
19377 AAAAAAAA
1 AAAAAAAC
19385 AACAAAAAC
1 AA-AAAAAC
19394 AAAAAAA
1 AAAAAAA
19401 AAGGAGAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:19401 original size:17 final size:19
Alignment explanation
Indices: 19354--19402 Score: 75
Period size: 17 Copynumber: 2.7 Consensus size: 19
19344 GTAAACACAC
19354 AAACAAAAAAAAACAAACA
1 AAACAAAAAAAAACAAACA
*
19373 AAACAAAAAAAAA-ACA-A
1 AAACAAAAAAAAACAAACA
19390 AAACAAAAAAAAA
1 AAACAAAAAAAAA
19403 GGAGAGAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 14 0.48
18 2 0.07
19 13 0.45
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (19 bp):
AAACAAAAAAAAACAAACA
Found at i:20731 original size:31 final size:31
Alignment explanation
Indices: 20696--20886 Score: 213
Period size: 31 Copynumber: 6.0 Consensus size: 31
20686 AATCTCTCTT
20696 CTCAAAGTCCACGACTCAGTGGCATCTTTTC
1 CTCAAAGTCCACGACTCAGTGGCATCTTTTC
* * *
20727 CTCAAAGTCCACAACTTAGTGGCATC-TCTC
1 CTCAAAGTCCACGACTCAGTGGCATCTTTTC
* *
20757 TTCAAAGTCCACGACTCATTGGCATCTTTTC
1 CTCAAAGTCCACGACTCAGTGGCATCTTTTC
* * * *
20788 TTCAAAGTCCATGACTTAGTGGCATATTTTC
1 CTCAAAGTCCACGACTCAGTGGCATCTTTTC
*
20819 TTCTTTAAAGTCCACGACTCAGTGGCATCTTTTTTTC
1 --C-TCAAAGTCCACGACTCAGTGGCATC---TTTTC
* *
20856 TTCAAAGTCCACGACTCAATGGCATCTTTTC
1 CTCAAAGTCCACGACTCAGTGGCATCTTTTC
20887 TCTTTCCAAA
Statistics
Matches: 133, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
30 25 0.19
31 59 0.44
34 44 0.33
37 5 0.04
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.35
Consensus pattern (31 bp):
CTCAAAGTCCACGACTCAGTGGCATCTTTTC
Found at i:20784 original size:61 final size:62
Alignment explanation
Indices: 20686--20851 Score: 226
Period size: 61 Copynumber: 2.6 Consensus size: 62
20676 CAATTCTTCA
20686 AATCTCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTCCTCAAAGTCCACAACTTAGTGGC
1 AATCTCTC-T-TCAAAGTCCACGACTCAGTGGCATCTTTTCCTCAAAGTCCACAACTTAGTGGC
* * **
20750 -ATCTCTCTTCAAAGTCCACGACTCATTGGCATCTTTTCTTCAAAGTCCATGACTTAGTGGC
1 AATCTCTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCCTCAAAGTCCACAACTTAGTGGC
* *
20811 ATATTTTCTTCTTTAAAGTCCACGACTCAGTGGCATCTTTT
1 A-A-TCTC-TCTTCAAAGTCCACGACTCAGTGGCATCTTTT
20852 TTTCTTCAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
61 49 0.54
62 1 0.01
63 8 0.09
64 3 0.03
65 30 0.33
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (62 bp):
AATCTCTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCCTCAAAGTCCACAACTTAGTGGC
Found at i:20829 original size:34 final size:33
Alignment explanation
Indices: 20697--20901 Score: 244
Period size: 34 Copynumber: 6.3 Consensus size: 33
20687 ATCTCTCTTC
20697 TCAAAGTCCACGACTCAGTGGCATCTTTTC-C-
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCTCT
* *
20728 TCAAAGTCCACAACTTAGTGGCATC---TCTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCTCT
*
20758 TCAAAGTCCACGACTCATTGGCATC-TTT-TCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCTCT
* * *
20789 TCAAAGTCCATGACTTAGTGGCATATTTTCTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTC-TCT
* *
20823 TTAAAGTCCACGACTCAGTGGCATCTTTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATC-TTTTCTCT
*
20857 TCAAAGTCCACGACTCAATGGCATCTTTTCTCTT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCTC-T
20891 TCCAAAGTCCA
1 T-CAAAGTCCA
20902 TAACTCCGTG
Statistics
Matches: 147, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.01
29 1 0.01
30 22 0.15
31 47 0.32
32 4 0.03
33 6 0.04
34 52 0.35
35 13 0.09
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.35
Consensus pattern (33 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTCTCT
Found at i:20954 original size:34 final size:33
Alignment explanation
Indices: 20916--21120 Score: 227
Period size: 34 Copynumber: 6.5 Consensus size: 33
20906 TCCGTGGCAC
20916 CCTTTTAAGCCCACAACTCCATGGCATTCTTTTT
1 CCTTTTAAGCCCACAACTCCATGGCA-TCTTTTT
* *
20950 CCTTTTAAGCCCACAACTCCGTGGTACTCTTTTT
1 CCTTTTAAGCCCACAACTCCATGGCA-TCTTTTT
* *
20984 CCTTTTAAGTCCACAACTCCGTGGCA-C-----
1 CCTTTTAAGCCCACAACTCCATGGCATCTTTTT
21011 CCTTTTAAGCCCACAACTCCATGGCATTCTTTTT
1 CCTTTTAAGCCCACAACTCCATGGCA-TCTTTTT
* *
21045 CCTTTTAAGTCCACAACTCCGTGGCA-C-----
1 CCTTTTAAGCCCACAACTCCATGGCATCTTTTT
* *
21072 CCTTTTAAGTCCACAACTCCATGGCATCTTTCT
1 CCTTTTAAGCCCACAACTCCATGGCATCTTTTT
21105 CCTTTTAAGCCCACAA
1 CCTTTTAAGCCCACAA
21121 GTTAGTGGCA
Statistics
Matches: 147, Mismatches: 11, Indels: 27
0.79 0.06 0.15
Matches are distributed among these distances:
27 49 0.33
28 1 0.01
29 1 0.01
32 2 0.01
33 15 0.10
34 79 0.54
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (33 bp):
CCTTTTAAGCCCACAACTCCATGGCATCTTTTT
Found at i:21002 original size:95 final size:95
Alignment explanation
Indices: 20895--21077 Score: 330
Period size: 95 Copynumber: 1.9 Consensus size: 95
20885 TCTCTTTCCA
*
20895 AAGTCCATAACTCCGTGGCACCCTTTTAAGCCCACAACTCCATGGCATTCTTTTTCCTTTTAAGC
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCATGGCATTCTTTTTCCTTTTAAGC
* *
20960 CCACAACTCCGTGGTACTCTTTTTCCTTTT
66 CCACAACTCCGTGGCACCCTTTTTCCTTTT
*
20990 AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCATGGCATTCTTTTTCCTTTTAAGT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCATGGCATTCTTTTTCCTTTTAAGC
21055 CCACAACTCCGTGGCACCCTTTT
66 CCACAACTCCGTGGCACCCTTTT
21078 AAGTCCACAA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (95 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCATGGCATTCTTTTTCCTTTTAAGC
CCACAACTCCGTGGCACCCTTTTTCCTTTT
Found at i:21015 original size:61 final size:60
Alignment explanation
Indices: 20950--21160 Score: 287
Period size: 61 Copynumber: 3.4 Consensus size: 60
20940 CATTCTTTTT
* *
20950 CCTTTTAAGCCCACAACTCCGTGGTACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
21011 CCTTTTAAGCCCACAACTCCATGGCATTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
* * * * **
21072 CCTTTTAAGTCCACAACTCCATGGCATCTTTCTCCTTTTAAGCCCACAAGTTAGTGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
* *
21132 CCTTTTCAAAAGCCCACAAGTCAATGGCA
1 CCTTTT---AAGCCCACAACTCCATGGCA
21161 GCCTTCAAAA
Statistics
Matches: 135, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
60 35 0.26
61 83 0.61
63 17 0.13
ACGTcount: A:0.23, C:0.33, G:0.13, T:0.31
Consensus pattern (60 bp):
CCTTTTAAGCCCACAACTCCATGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:21147 original size:30 final size:29
Alignment explanation
Indices: 21111--21207 Score: 106
Period size: 30 Copynumber: 3.3 Consensus size: 29
21101 TTCTCCTTTT
21111 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGTGGCACCC-TTTCAA
* * *
21141 AAGCCCACAAGTCAATGGCAGCC-TTCAA
1 AAGCCCACAAGTTAGTGGCACCCTTTCAA
* * **
21169 AAGCACAACAAGTTGGTGTAACCCTTTCAA
1 AAGC-CCACAAGTTAGTGGCACCCTTTCAA
21199 AAGCCCACA
1 AAGCCCACA
21208 TAAGTTGGTG
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
28 9 0.17
29 16 0.30
30 29 0.54
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (29 bp):
AAGCCCACAAGTTAGTGGCACCCTTTCAA
Found at i:21437 original size:52 final size:49
Alignment explanation
Indices: 21324--21952 Score: 578
Period size: 49 Copynumber: 12.5 Consensus size: 49
21314 ACAAGCCCAG
* * * * *
21324 TATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCGA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* * * * * * *
21373 TGTTGTTGGCCTTGAATCAGTACATCGGCACCTCAACCATCTTTAAGCCCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACCT---TCATCTTTAAGTCCAA
* *
21425 TATTGCTGGCCTTGAATCAGCATATTGGCA--TATCATCTTTAAGTCCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACCT-TCATCTTTAAGTCCAA
* * *
21473 TGTCGCTGGCCTTGAATCAGTACATTGGCACCTTTATCTTTAAGTCCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* * * * *
21522 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTTATCTTTAGGACCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAA
* *
21574 TGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* * *
21623 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATTTTTAAGTCCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAA
* * *
21675 TGTCGTTGGCCTTGAATCAGCACATTGACACCTTCATCTTTAAGTCCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* * ** * *
21724 TATCGCTGGCCTTGAATCAACATATTGGCGTGTTCGTCACCTTTAAGTCCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGC---ACCTTCATCTTTAAGTCCAA
* * *
21776 TGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAATCCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* * **
21825 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCATCTTT-AAGTCCAA
* * * * * * *
21878 TGTCGTTGGCCTTTAATCAGCATATTGGCATTCTTCTCATCTTCAAGTCTAA
1 TATCGCTGGCCTTGAATCAGCACATTGGCA--CCT-TCATCTTTAAGTCCAA
* * * *
21930 TGTCGCTGACCGTGAATTAGCAC
1 TATCGCTGGCCTTGAATCAGCAC
21953 TTTGACATCC
Statistics
Matches: 476, Mismatches: 84, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
48 41 0.09
49 194 0.41
50 5 0.01
51 2 0.00
52 192 0.40
53 40 0.08
54 1 0.00
55 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
TATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
Found at i:21605 original size:101 final size:101
Alignment explanation
Indices: 21324--21907 Score: 786
Period size: 101 Copynumber: 5.8 Consensus size: 101
21314 ACAAGCCCAG
* * * *
21324 TATCGTTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAAGACCGATGTTGTTGGCCTT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTT
* * * *
21386 GAATCAGTACATCGGCACCTCAACCATCTTTAAGCCCAA
66 GAATCAGCACATTGGCACCT---TCATCTTTAAGTCCAA
* * * * *
21425 TATTGCTGGCCTTGAATCAGCATATT-G-G-C-ATATCATCTTTAAGTCCAATGTCGCTGGCCTT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTT
* *
21486 GAATCAGTACATTGGCACCTTTATCTTTAAGTCCAA
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* * * *
21522 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTTATCTTTAGGACCAATGTCGCTAGCCTT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTT
21587 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* *
21623 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATTTTTAAGTCCAATGTCGTTGGCCTT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTT
*
21688 GAATCAGCACATTGACACCTTCATCTTTAAGTCCAA
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* ** * * *
21724 TATCGCTGGCCTTGAATCAACATATTGGCGTGTTCGTCACCTTTAAGTCCAATGTCGTTGGCCTT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTT
*
21789 GAATCAGCACATTGGCACCTTCATCTTTAAATCCAA
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
* *
21825 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAATGTCGTTGGCCT
1 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGA-CCAATGTCGTTGGCCT
* *
21890 TTAATCAGCATATTGGCA
65 TGAATCAGCACATTGGCA
21908 TTCTTCTCAT
Statistics
Matches: 432, Mismatches: 44, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
97 38 0.09
98 3 0.01
99 2 0.00
100 44 0.10
101 313 0.72
102 32 0.07
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (101 bp):
TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGACCAATGTCGTTGGCCTT
GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
Found at i:22849 original size:29 final size:27
Alignment explanation
Indices: 22777--22849 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
22767 AAATTTATGT
* *
22777 ATTTATTAGATTATTATAAAATATAAA
1 ATTTATTACATTATTATAAAAAATAAA
*
22804 ATTTATATATTCATTA-TATAATAAATAAA
1 ATTTAT-TA--CATTATTATAAAAAATAAA
*
22833 ATTTATTACATTTTTAT
1 ATTTATTACATTATTAT
22850 TTACATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 4 0.11
27 9 0.24
28 4 0.11
29 17 0.45
30 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (27 bp):
ATTTATTACATTATTATAAAAAATAAA
Found at i:25852 original size:38 final size:38
Alignment explanation
Indices: 25801--25874 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
25791 TCTCCATTTT
25801 TAGATTGCATAATGTAAGCTCTTGAAAATGACAAAATG
1 TAGATTGCATAATGTAAGCTCTTGAAAATGACAAAATG
*
25839 TAGATTGCATAATGTAAGCTCTTGAAAATGAGAAAA
1 TAGATTGCATAATGTAAGCTCTTGAAAATGACAAAA
25875 ATGGTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.28
Consensus pattern (38 bp):
TAGATTGCATAATGTAAGCTCTTGAAAATGACAAAATG
Found at i:28386 original size:13 final size:13
Alignment explanation
Indices: 28368--28397 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
28358 ACAAATCTTC
28368 ATGTATCGATACA
1 ATGTATCGATACA
28381 ATGTATCGATACA
1 ATGTATCGATACA
28394 ATGT
1 ATGT
28398 CCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:28389 original size:33 final size:33
Alignment explanation
Indices: 28347--28413 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
28337 CATTGGGCAT
*
28347 AATGTATCGATACAAATCT-TCATGTATCGATAC
1 AATGTATCGATAC-AATCTCCCATGTATCGATAC
*
28380 AATGTATCGATACAATGTCCCATGTATCGATAC
1 AATGTATCGATACAATCTCCCATGTATCGATAC
28413 A
1 A
28414 TTTCACATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 4 0.13
33 27 0.87
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (33 bp):
AATGTATCGATACAATCTCCCATGTATCGATAC
Found at i:28482 original size:13 final size:13
Alignment explanation
Indices: 28464--28488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28454 TAATTGAGTG
28464 TGTATCGATACAT
1 TGTATCGATACAT
28477 TGTATCGATACA
1 TGTATCGATACA
28489 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:30686 original size:21 final size:20
Alignment explanation
Indices: 30636--30688 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
30626 GTGTTTTTGT
30636 TGATG-ATTTTGATGAAAAA
1 TGATGAATTTTGATGAAAAA
* *
30655 TAGAT-AGTTTTGATGTGAAAA
1 T-GATGAATTTTGATG-AAAAA
30676 TGATGAATTTTGA
1 TGATGAATTTTGA
30689 AAAGGATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.04
20 14 0.52
21 12 0.44
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (20 bp):
TGATGAATTTTGATGAAAAA
Found at i:30828 original size:13 final size:13
Alignment explanation
Indices: 30810--30835 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30800 ATATTGACAT
30810 AATGTATCGATAC
1 AATGTATCGATAC
30823 AATGTATCGATAC
1 AATGTATCGATAC
30836 TTAGAACATT
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):
AATGTATCGATAC
Found at i:37892 original size:20 final size:20
Alignment explanation
Indices: 37864--37904 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
37854 CACATATTGC
37864 TAAGGAAATGTATCGATACA
1 TAAGGAAATGTATCGATACA
*
37884 TAAGTAAATGTATCGATACA
1 TAAGGAAATGTATCGATACA
37904 T
1 T
37905 TCACTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (20 bp):
TAAGGAAATGTATCGATACA
Found at i:40401 original size:79 final size:78
Alignment explanation
Indices: 40318--40555 Score: 264
Period size: 79 Copynumber: 3.0 Consensus size: 78
40308 TTCTAGTCCC
* *
40318 GTTATTTCCGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACTAATTTTCCATCACCGGG
1 GTTATTTCTGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACTAATTTTCCA-CATCGGG
*
40383 GATACTCTAACCCT
65 GATACTCCAACCCT
* * * * *
40397 GTTATTTCTAAGGGGATACTCCAACC-CCAGTTTTATTTCTAAAACACCAATTTTTCACAATTGG
1 GTTATTTCTGAGGGGATACTCCAACCTCGA-TTTTATTTCTAAAACACTAATTTTCCAC-ATCGG
*
40461 GGATACTCCAACCCC
64 GGATACTCCAACCCT
* ** * * * **
40476 GTTATTTTTGAAAGGATACTCTAACCTCGGTTTTATTT-TCAAAACACTGATTTTCCACCATCAA
1 GTTATTTCTGAGGGGATACTCCAACCTCGATTTTATTTCT-AAAACACTAATTTTCCA-CATCGG
40540 GGATACTCCAACCCT
64 GGATACTCCAACCCT
40555 G
1 G
40556 ATTTTACTTC
Statistics
Matches: 131, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
78 4 0.03
79 125 0.95
80 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (78 bp):
GTTATTTCTGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACTAATTTTCCACATCGGGG
ATACTCCAACCCT
Found at i:40561 original size:51 final size:52
Alignment explanation
Indices: 40487--40603 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 52
40477 TTATTTTTGA
* * * *
40487 AAGGATACTCTAA-CCTCGGTTTTA-TTTTCAAAACACTGATTTTCCACCATC
1 AAGGATACTCCAACCCTCGATTTTACTTCT-AAAACACTAATTTTCCACCATC
*
40538 AAGGATACTCCAACCCT-GATTTTACTTCTGAAACACTAATTTTCCACCATC
1 AAGGATACTCCAACCCTCGATTTTACTTCTAAAACACTAATTTTCCACCATC
**
40589 GGGGATACTCCAACC
1 AAGGATACTCCAACC
40604 TTGTTATTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 51 0.89
52 6 0.11
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (52 bp):
AAGGATACTCCAACCCTCGATTTTACTTCTAAAACACTAATTTTCCACCATC
Found at i:40579 original size:130 final size:129
Alignment explanation
Indices: 40410--40683 Score: 340
Period size: 130 Copynumber: 2.1 Consensus size: 129
40400 ATTTCTAAGG
* * *
40410 GGATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTTTTCACAATTGGGGATACTCCAACCC
1 GGATACTCCAACCCCAGTTTTACTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCC
* * *
40475 CGTTATTTTTGAA-AGGATACTCTAACCTCGGTTTTATTT-TCAAAACA-CTGATTTTCCACCAT
66 CGTTATTTCTGAAGA-GATACTCTAACCCCGGTTTTATTTCT-AAAACATC-GATTTTCC-CAAT
40537 CAA
127 CAA
* * * *
40540 GGATACTCCAA-CCCTGATTTTACTTCTGAAACACTAATTTTCCACCATCGGGGATACTCCAACC
1 GGATACTCCAACCCCAG-TTTTACTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACC
** * *
40604 TTGTTATTTCTGAGGAGATACTCTAACCCCGGTTTTATTTCTAAAACATCGATTTTCCCAATCAG
65 CCGTTATTTCTGAAGAGATACTCTAACCCCGGTTTTATTTCTAAAACATCGATTTTCCCAATCAA
*
40669 GGATACTTCAACCCC
1 GGATACTCCAACCCC
40684 GTTATTTTTG
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
129 19 0.15
130 102 0.82
131 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (129 bp):
GGATACTCCAACCCCAGTTTTACTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCC
CGTTATTTCTGAAGAGATACTCTAACCCCGGTTTTATTTCTAAAACATCGATTTTCCCAATCAA
Found at i:40767 original size:157 final size:159
Alignment explanation
Indices: 40540--40896 Score: 422
Period size: 157 Copynumber: 2.3 Consensus size: 159
40530 CCACCATCAA
* * * *
40540 GGATACTCCAACC-CTGATTTTA-CTTCTGAAACA-CTAATTTTCCACCATCGGGGATACTCCAA
1 GGATACTCCAACCTC-GATTTTATTTTC-AAAACATCAAATTTTCCACCATCGAGGATACTCCAA
* * * *
40602 CCTTGTTATTTCTGAGGAGATACTCTAACCCCGGTTTTA-TTTCTAAAACATCGATTTTCC-CAA
64 CCTCGTTATTTCTGAGGAGATACTCTAACCCCGATTTTATTTTC-AAAACACCAATTTTCCACAA
* *
40665 TCAGGGATACTTCAACCCCGTTATTTTTGAGG
128 TCAGGGATACTCCAACCCCGTTATTTCTGAGG
*
40697 GGATACTCCAACCTCGATTTTATTTTCAAAACATCAAATTTT-CACCATCGAGGATACTCTAACC
1 GGATACTCCAACCTCGATTTTATTTTCAAAACATCAAATTTTCCACCATCGAGGATACTCCAACC
* * * **
40761 TCGTTATTTTTGAGGGGATACTCTAACCCCGATTTTATTTTCAAAACACCAATTTTCCACCATTG
66 TCGTTATTTCTGAGGAGATACTCTAACCCCGATTTTATTTTCAAAACACCAATTTTCCACAATCA
*
40826 GGGATACTCCAACCTCGTTATTTCTGAGG
131 GGGATACTCCAACCCCGTTATTTCTGAGG
* * * * * *
40855 GGATACTTCAATCTTGTTTTTATCTTT-AAAATATTAAATTTT
1 GGATACTCCAACCTCGATTTTAT-TTTCAAAACATCAAATTTT
40897 TCATCGGGGG
Statistics
Matches: 171, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
157 92 0.54
158 76 0.44
159 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (159 bp):
GGATACTCCAACCTCGATTTTATTTTCAAAACATCAAATTTTCCACCATCGAGGATACTCCAACC
TCGTTATTTCTGAGGAGATACTCTAACCCCGATTTTATTTTCAAAACACCAATTTTCCACAATCA
GGGATACTCCAACCCCGTTATTTCTGAGG
Found at i:40818 original size:287 final size:286
Alignment explanation
Indices: 40318--40839 Score: 703
Period size: 287 Copynumber: 1.8 Consensus size: 286
40308 TTCTAGTCCC
* *
40318 GTTATTTCCGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACACTAATTTTCCATCACCGGG
1 GTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCATCA-C-GG
* *
40383 GATACTCTAACCCTGTTATTTCTAAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCAAT
64 GATACTCTAACCCCGTTATTTCTAAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCAAA
* * * *
40448 TTTTCACAATTGGGGATACTCCAACCCCGTTATTTTTGAAAGGATACTCTAACCTCGGTTTTATT
129 TTTTCACAATCGAGGATACTCCAACCCCGTTATTTTTGAAAGGATACTCTAACCCCGATTTTATT
**
40513 TTCAAAACACTGATTTTCCACCATCAAGGATACTCCAACCCTGATTTTACTTCTGAAACACTAAT
194 TTCAAAACACCAATTTTCCACCATCAAGGATACTCCAACCCTGATTTTACTTCTGAAACACTAAT
40578 TTTCCACCATCGGGGATACTCCAACCTT
259 TTTCCACCATCGGGGATACTCCAACCTT
* * * *
40606 GTTATTTCTGAGGAGATACTCTAACCCCGGTTTTATTTCTAAAACA-TCGATTTTCCCAATCA-G
1 GTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACACT-AATTTT-CC-ATCACG
* * * *
40669 GGATACT-TCAACCCCGTTATTTTTGAGGGGATACTCCAACCTC-GATTTTATTT-TCAAAACAT
63 GGATACTCT-AACCCCGTTATTTCTAAGGGGATACTCCAACCCCAG-TTTTATTTCT-AAAACAC
* * * **
40731 CAAATTTTCACCATCGAGGATACTCTAACCTCGTTATTTTTGAGGGGATACTCTAACCCCGATTT
125 CAAATTTTCACAATCGAGGATACTCCAACCCCGTTATTTTTGAAAGGATACTCTAACCCCGATTT
***
40796 TATTTTCAAAACACCAATTTTCCACCATTGGGGATACTCCAACC
190 TATTTTCAAAACACCAATTTTCCACCATCAAGGATACTCCAACC
40840 TCGTTATTTC
Statistics
Matches: 202, Mismatches: 26, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
286 3 0.01
287 147 0.73
288 46 0.23
289 2 0.01
290 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (286 bp):
GTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCATCACGGGA
TACTCTAACCCCGTTATTTCTAAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCAAATT
TTCACAATCGAGGATACTCCAACCCCGTTATTTTTGAAAGGATACTCTAACCCCGATTTTATTTT
CAAAACACCAATTTTCCACCATCAAGGATACTCCAACCCTGATTTTACTTCTGAAACACTAATTT
TCCACCATCGGGGATACTCCAACCTT
Found at i:40877 original size:79 final size:79
Alignment explanation
Indices: 40540--40861 Score: 391
Period size: 79 Copynumber: 4.1 Consensus size: 79
40530 CCACCATCAA
* * * * *
40540 GGATACTCCAACCCTGATTTTA-CTTCTGAAACACTAATTTTCCACCATCGGGGATACTCCAACC
1 GGATACTCTAACCCCGATTTTATTTTC-AAAACACCAATTTTCCACCATCGGGGATACTCCAACC
*
40604 TTGTTATTTCTGAGG
65 TCGTTATTTCTGAGG
* * * * * * *
40619 AGATACTCTAACCCCGGTTTTA-TTTCTAAAACATCGATTTTCC-CAATCAGGGATACTTCAACC
1 GGATACTCTAACCCCGATTTTATTTTC-AAAACACCAATTTTCCACCATCGGGGATACTCCAACC
* *
40682 CCGTTATTTTTGAGG
65 TCGTTATTTCTGAGG
* * * * *
40697 GGATACTCCAACCTCGATTTTATTTTCAAAACATCAAATTTT-CACCATCGAGGATACTCTAACC
1 GGATACTCTAACCCCGATTTTATTTTCAAAACA-CCAATTTTCCACCATCGGGGATACTCCAACC
*
40761 TCGTTATTTTTGAGG
65 TCGTTATTTCTGAGG
*
40776 GGATACTCTAACCCCGATTTTATTTTCAAAACACCAATTTTCCACCATTGGGGATACTCCAACCT
1 GGATACTCTAACCCCGATTTTATTTTCAAAACACCAATTTTCCACCATCGGGGATACTCCAACCT
40841 CGTTATTTCTGAGG
66 CGTTATTTCTGAGG
40855 GGATACT
1 GGATACT
40862 TCAATCTTGT
Statistics
Matches: 204, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
78 61 0.30
79 143 0.70
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (79 bp):
GGATACTCTAACCCCGATTTTATTTTCAAAACACCAATTTTCCACCATCGGGGATACTCCAACCT
CGTTATTTCTGAGG
Found at i:42909 original size:4 final size:4
Alignment explanation
Indices: 42900--42947 Score: 78
Period size: 4 Copynumber: 11.8 Consensus size: 4
42890 TATTGAGGTG
*
42900 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTCA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTT
42948 GTTTTGTGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
4 37 0.90
5 4 0.10
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Done.