Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2055
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: 47920
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1622 original size:54 final size:54
Alignment explanation
Indices: 1540--1717 Score: 207
Period size: 55 Copynumber: 3.3 Consensus size: 54
1530 ATATTGAGCC
* * * *
1540 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * * *
1594 CGCACACTT-GTGCTACATAGTCAGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
1648 CGCACACTTAGTGC-ATCATATTTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATA-ATCAACTCGCACACTTAGTGCCACATAGTCAAAT
1703 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1718 GTACAATTTA
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
53 12 0.12
54 43 0.41
55 46 0.44
56 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:1686 original size:28 final size:27
Alignment explanation
Indices: 1540--1716 Score: 167
Period size: 27 Copynumber: 6.5 Consensus size: 27
1530 ATATTGAGCC
* * * * *
1540 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCAACATAGTCAATT
* * * *
1567 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCAACATAGTCAATT
* *
1594 CGCACACTT-GTGCTACATAGTCAGACT
1 CGCACACTTAGTGCAACATAGTCA-ATT
** *
1621 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAACATAGTCAATT
* * *
1648 CGCACACTTAGTGCATCATATTTCATTT
1 CGCACACTTAGTGCAACATA-GTCAATT
*
1676 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCAACATAGTCAATT
1703 CGCACACTTAGTGC
1 CGCACACTTAGTGC
1717 TGTACAATTT
Statistics
Matches: 125, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
26 11 0.09
27 79 0.63
28 35 0.28
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCAACATAGTCAATT
Found at i:9492 original size:27 final size:27
Alignment explanation
Indices: 9462--9638 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
9452 ATATTGAGCC
* *
9462 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
9489 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
9516 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
9544 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
9571 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
9598 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
9625 CGCAC-CTTAGTGCT
1 CGCACACTTAGTGCT
9639 GTACAATTTA
Statistics
Matches: 124, Mismatches: 23, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
26 7 0.06
27 93 0.75
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:9601 original size:82 final size:80
Alignment explanation
Indices: 9483--9637 Score: 204
Period size: 82 Copynumber: 1.9 Consensus size: 80
9473 TGCTATATAA
* * * *
9483 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCA-AATCGCA
9548 CACTTAGTGCCGCATGG
65 C-CTTAGTGCCGCATGG
* * **
9565 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
9629 CCTTAGTGC
65 CCTTAGTGC
9638 TGTACAATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 8 0.12
81 9 0.14
82 47 0.73
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
CTTAGTGCCGCATGG
Found at i:11644 original size:46 final size:46
Alignment explanation
Indices: 11526--11636 Score: 177
Period size: 46 Copynumber: 2.4 Consensus size: 46
11516 TCTGAACTCA
* *
11526 TTGAGTTGAGCCCGAGTTCACTTATGGATGCGAGCACCCGAGCTCG
1 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCG
* * *
11572 CTGAGCTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCG
1 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCG
11618 TTGAGTTGAGTCCGAGTTC
1 TTGAGTTGAGTCCGAGTTC
11637 GTATATGGGT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (46 bp):
TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCG
Found at i:13916 original size:138 final size:138
Alignment explanation
Indices: 13495--14183 Score: 941
Period size: 138 Copynumber: 5.1 Consensus size: 138
13485 TAGAAAAATG
* * * *
13495 AATTATATTCTTT-TAGAAAAAA-ATTAATTTCCATATCTTTTATATTTTGACTAAAATTATTTA
1 AATTATATTCTTTCCA-AAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTA
* * * * *
13558 ATGTAAC----TATTTTAATAAATTCAGTAAAATATATACAATTAATAGTTTATATGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
13619 TCATATATT
130 TCATATATT
** **
13628 AATTATATTCTTT-CAAACGGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTA
1 AATTATATTCTTTCCAAA-AAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTA
* * ** *
13692 TTATAACTATTTATATTAATAAATTTAGTAATATATATA-AA-TAATATTTTGTATGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
13755 TCATATATT
130 TCATATATT
* * * * * *
13764 AATTATATTATTTCCAAAAAAATAATAATTTTCATATCTTGTATATTTTGATTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
13829 TATAATTGTGTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
13894 CATAAATT
131 CATATATT
* *
13902 AATTATATTCTTTCCAAAAGAATATTAATTCCCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
*
13967 TATAACTGTTTATATTAATAAATTCGGAAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
14032 CATATATT
131 CATATATT
* * * * *
14040 AATTATATTATTTCGAAAATAATATTAACTTCCATGTCTTTTATA-TTTGACTGAAGTTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* * *
14104 TATAACTGTTTATATTAAAAAATTCGGTAAAATATATAAAATTAATATTTTGCATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
14169 CATATATT
131 CATATATT
14177 -ATTATAT
1 AATTATAT
14184 CTATGTTCTC
Statistics
Matches: 494, Mismatches: 53, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
132 2 0.00
133 16 0.03
134 43 0.09
136 117 0.24
137 95 0.19
138 221 0.45
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:14183 original size:274 final size:272
Alignment explanation
Indices: 13495--14183 Score: 969
Period size: 274 Copynumber: 2.5 Consensus size: 272
13485 TAGAAAAATG
* * * *
13495 AATTATATTCTTTTAGAAAAAA-ATTAATTTCCATATCTTTTATATTTTGACTAAAATTATTTAA
1 AATTATATT-ATTTCGAAAAAATATTAATTTCCATATCTTTTATATTTTGACTGAAATTAATTAA
* * * * *
13559 TGTAAC---TATTTTAATAAATTCAGTAAAATATATACAATTAATAGTTTATATGAATCAAATTC
65 TATAACTGTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
* *
13621 ATATATTAATTATATTCTTTCAAACGGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAAT
130 ATATATTAATTATATTCTTTCAAACAGAATATTAATTCCCATGTCTTTTATATTTTGACCAAAAT
* * * *
13686 TAATTATTATAACTATTTATATTAATAAATTTAGTAATATATATAAATAATATTTTGTATGAATC
195 TAATTAATATAACTATTTATATTAATAAATTCAGAAAAATATATAAATAATATTTTGTATGAATC
13751 AAATTCATATATT
260 AAATTCATATATT
* * * * *
13764 AATTATATTATTTCCAAAAAAATAATAATTTTCATATCTTGTATATTTTGATTGAAATTAATTAA
1 AATTATATTATTT-CGAAAAAATATTAATTTCCATATCTTTTATATTTTGACTGAAATTAATTAA
*
13829 TATAATTGTGTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
65 TATAACTGT-TATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
* **
13894 CATAAATTAATTATATTCTTTCCAAA-AGAATATTAATTCCCATGTCTTTTATATTTTGACTGAA
129 CATATATTAATTATATTCTTT-CAAACAGAATATTAATTCCCATGTCTTTTATATTTTGACCAAA
* *
13958 ATTAATTAATATAACTGTTTATATTAATAAATTCGGAAAAATATATACAATTAATATTTTGTATG
193 ATTAATTAATATAACTATTTATATTAATAAATTCAGAAAAATATATA-AA-TAATATTTTGTATG
14023 AATCAAATTCATATATT
256 AATCAAATTCATATATT
* * *
14040 AATTATATTATTTCGAAAATAATATTAACTTCCATGTCTTTTATA-TTTGACTGAAGTTAATTAA
1 AATTATATTATTTCGAAAA-AATATTAATTTCCATATCTTTTATATTTTGACTGAAATTAATTAA
* * *
14104 TATAACTGTTTATATTAAAAAATTCGGTAAAATATATAAAATTAATATTTTGCATGAATCAAATT
65 TATAACTG-TTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
14169 CATATATT-ATTATAT
129 CATATATTAATTATAT
14184 CTATGTTCTC
Statistics
Matches: 370, Mismatches: 39, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
268 3 0.01
269 15 0.04
270 40 0.11
274 153 0.41
275 94 0.25
276 65 0.18
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (272 bp):
AATTATATTATTTCGAAAAAATATTAATTTCCATATCTTTTATATTTTGACTGAAATTAATTAAT
ATAACTGTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCA
TATATTAATTATATTCTTTCAAACAGAATATTAATTCCCATGTCTTTTATATTTTGACCAAAATT
AATTAATATAACTATTTATATTAATAAATTCAGAAAAATATATAAATAATATTTTGTATGAATCA
AATTCATATATT
Found at i:18029 original size:40 final size:40
Alignment explanation
Indices: 17985--18117 Score: 110
Period size: 40 Copynumber: 3.1 Consensus size: 40
17975 ATTAACTAAC
17985 CACATATCAATACCATGTCATTAAACAACTATCAACGCAA
1 CACATATCAATACCATGTCATTAAACAACTATCAACGCAA
* * * * *
18025 CACATAAT-AGTTAACA-GTACACCTTATACATTACCTAATTAAC-TAA
1 CACAT-ATCA-ATACCATGT-CA--TTAAACA--A-CT-ATCAACGCAA
18071 CCACATATCAATACCATGTCATTAAACAACTATCAACGCAA
1 -CACATATCAATACCATGTCATTAAACAACTATCAACGCAA
18112 CACATA
1 CACATA
18118 AAGACCTAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 26
0.66 0.09 0.25
Matches are distributed among these distances:
40 19 0.27
41 12 0.17
42 1 0.01
43 6 0.09
44 6 0.09
45 1 0.01
46 12 0.17
47 13 0.19
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.25
Consensus pattern (40 bp):
CACATATCAATACCATGTCATTAAACAACTATCAACGCAA
Found at i:18096 original size:87 final size:87
Alignment explanation
Indices: 17945--18118 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 87
17935 GACCATTCCT
17945 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
1 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
18010 CAACTATCAACGCAACACATAA
66 CAACTATCAACGCAACACATAA
*
18032 TAGTTAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
1 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
18097 CAACTATCAACGCAACACATAA
66 CAACTATCAACGCAACACATAA
18119 AGACCTAATT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (87 bp):
TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
CAACTATCAACGCAACACATAA
Found at i:19166 original size:43 final size:44
Alignment explanation
Indices: 19106--19237 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 44
19096 CACATAAATC
*
19106 ATACAATGCCAACGTCCCAGTCGTGGTCTTACATGTAATCACAT
1 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACAT
* * * *
19150 ATA-GATGCC-ACTGTCCCAAACAG-GATCTTACACGTAATCACAT
1 ATACAATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCACAT
*
19193 A-ACAATGCCAACGTCCCAGACGTGGTATTACATG-AATACACAT
1 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAAT-CACAT
19236 AT
1 AT
19238 CGAAATTCTA
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
42 7 0.10
43 58 0.82
44 6 0.08
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (44 bp):
ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACAT
Found at i:19557 original size:15 final size:15
Alignment explanation
Indices: 19537--19572 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
19527 GTTCTTGATT
19537 TTCAAATTAAACCCA
1 TTCAAATTAAACCCA
*
19552 TTCAAATTAAACTCA
1 TTCAAATTAAACCCA
19567 TTCAAA
1 TTCAAA
19573 CATAATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (15 bp):
TTCAAATTAAACCCA
Found at i:23586 original size:51 final size:51
Alignment explanation
Indices: 23503--23640 Score: 165
Period size: 51 Copynumber: 2.7 Consensus size: 51
23493 GATGCCCGAC
*
23503 GGCCTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTCTTCACA-A-AGT
1 GGCCTGCACATAGTACCACACTTGTGA-TCAAAGCTACC-T-TTCACACATAGT
* * *
23554 GGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCACACATAGT
1 GGCCTGCACATAGTACCACACTTGTGATCAAAGCTACCTTTCACACATAGT
* * *
23605 GGCCTGCACTTAGTACCACACATGTGATCGAAGCTA
1 GGCCTGCACATAGTACCACACTTGTGATCAAAGCTA
23641 TCGGGTACAC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
49 6 0.08
50 2 0.03
51 66 0.88
52 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (51 bp):
GGCCTGCACATAGTACCACACTTGTGATCAAAGCTACCTTTCACACATAGT
Found at i:23641 original size:51 final size:52
Alignment explanation
Indices: 23503--23721 Score: 164
Period size: 51 Copynumber: 4.3 Consensus size: 52
23493 GATGCCCGAC
* * * * * * * *
23503 GGCCTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTC-TTCACAAAGT
1 GGCCTGCACTTAGTACCACACATGTGA-CCAAAGCTATCGTCGTACACATAGT
* * * *
23554 GGCCTTCACATAGTACCACACTTGTGACCAAAGCTATC-T-TTCACACATAGT
1 GGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCGTCGT-ACACATAGT
* * *
23605 GGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCG-GGTACACATAGT
1 GGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCGTCGTACACATAGT
* * * * * * *
23656 AGCCTACACTTAGTACTACACATGCGACCTAA-CTATC-TGGTACACGTAGT
1 GGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCGTCGTACACATAGT
*
23706 AGCCTGCACTTAGTAC
1 GGCCTGCACTTAGTAC
23722 TATACACGTG
Statistics
Matches: 142, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
50 33 0.23
51 107 0.75
52 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (52 bp):
GGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCGTCGTACACATAGT
Found at i:23706 original size:50 final size:51
Alignment explanation
Indices: 23546--23783 Score: 192
Period size: 51 Copynumber: 4.7 Consensus size: 51
23536 CTACCTTCTT
* * * * * * * **
23546 CACAAAGTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATC-TTTCA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCTATCGGGT-A
* * * *
23597 CACATAGTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCTATCGGGTA
* * *
23648 CACATAGTAGCCTACACTTAGTACTACACATGCGACCTAA-CTATCTGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCTATCGGGTA
* * * * * *****
23698 CACGTAGTAGCCTGCACTTAGTACTATACACGTGACCTAAAACTGTTTTAAA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCT-AAGCTATCGGGTA
* *
23750 CACATTGTAGCCTGCACATAGTACTACACATGTG
1 CACATAGTAGCCTGCACTTAGTACTACACATGTG
23784 TTCTCACAAC
Statistics
Matches: 154, Mismatches: 30, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
50 42 0.27
51 77 0.50
52 35 0.23
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (51 bp):
CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCTATCGGGTA
Found at i:27116 original size:48 final size:48
Alignment explanation
Indices: 27060--27193 Score: 169
Period size: 48 Copynumber: 2.8 Consensus size: 48
27050 AGATCCCGTA
* * * **
27060 TAAGACCATATCTAGGATATGACATCAGCATCGATATGTGACCCCATG
1 TAAGACCATGTCTAGGACATGGCATTGGCATCGATATGTGACCCCATG
* * * * *
27108 TAAGACCATGTATGGGACATGGCATTGGCACCGTTATGTGATCCCATG
1 TAAGACCATGTCTAGGACATGGCATTGGCATCGATATGTGACCCCATG
*
27156 TAAGATCATGTCTAGGACATGGCATTGGCATCGATATG
1 TAAGACCATGTCTAGGACATGGCATTGGCATCGATATG
27194 AGAACATCGT
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (48 bp):
TAAGACCATGTCTAGGACATGGCATTGGCATCGATATGTGACCCCATG
Found at i:30156 original size:27 final size:27
Alignment explanation
Indices: 30134--30209 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
30124 TCATCCTATA
*
30134 TTTACTATCCTGATGGACTATCCCGTG
1 TTTACTATCCTGATGGACTATCCCATG
* * * *
30161 TTTACTGTCTTGATGAAATATCCCATG
1 TTTACTATCCTGATGGACTATCCCATG
*
30188 TTTACTATCCCGATGGACTATC
1 TTTACTATCCTGATGGACTATC
30210 TATGTTGTCG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (27 bp):
TTTACTATCCTGATGGACTATCCCATG
Found at i:33847 original size:79 final size:81
Alignment explanation
Indices: 33711--33895 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
33701 TTGAATGATG
* *
33711 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
33775 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
33790 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
33852 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
33870 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
33896 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:33909 original size:40 final size:40
Alignment explanation
Indices: 33712--33895 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
33702 TGAATGATGT
* * * *
33712 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
33752 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
33792 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
33830 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
33871 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
33896 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:33917 original size:79 final size:79
Alignment explanation
Indices: 33764--33928 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
33754 GGACTAAGAT
* * **
33764 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
33829 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
33843 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
33906 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
33922 CCGAAGG
1 CCGAAGG
33929 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:40494 original size:20 final size:20
Alignment explanation
Indices: 40429--40494 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
40419 TGGTTGAGCA
40429 TCCGAACTCGTTGAGTTGAG
1 TCCGAACTCGTTGAGTTGAG
** * *
40449 TCCGAGTTCACTT-A-TGGAATG
1 TCCGAACTC-GTTGAGTTG-A-G
40470 TCCGAACTCGTTGAGTTGAG
1 TCCGAACTCGTTGAGTTGAG
40490 TCCGA
1 TCCGA
40495 GTTCGTGAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
19 2 0.06
20 17 0.52
21 12 0.36
22 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (20 bp):
TCCGAACTCGTTGAGTTGAG
Found at i:40521 original size:46 final size:43
Alignment explanation
Indices: 40426--40598 Score: 183
Period size: 46 Copynumber: 3.9 Consensus size: 43
40416 GGATGGTTGA
*
40426 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAATGGAAT
* *
40469 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-AATGGAA-T
*
40511 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG-AT
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAATGGAAT
* * *
40555 GCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GC--A--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAATGG
40599 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
40 1 0.01
41 34 0.31
42 3 0.03
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.60
47 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (43 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAATGGAAT
Found at i:40529 original size:87 final size:91
Alignment explanation
Indices: 40426--40590 Score: 266
Period size: 87 Copynumber: 1.8 Consensus size: 91
40416 GGATGGTTGA
* *
40426 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-T-T-ATG-GAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGCCCGAACTCGTTGAGTT
40487 GAGTCCGAGTTCGTGAATGTAACTAG
66 GAGTCCGAGTTCGTGAATGTAACTAG
*
40513 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAACGCCCGAACTCGTTGAGT
40578 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
40591 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
87 34 0.49
88 1 0.01
89 1 0.01
91 3 0.04
92 31 0.44
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.28
Consensus pattern (91 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAATGTAACTAG
Found at i:44403 original size:21 final size:23
Alignment explanation
Indices: 44378--44420 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
44368 GTTGGTGTTT
44378 TTGGTT-TTTTTTTT-TTTTTTC
1 TTGGTTCTTTTTTTTGTTTTTTC
44399 TTGGTTCTTTTTTTTGTTTTTT
1 TTGGTTCTTTTTTTTGTTTTTT
44421 TTACATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 8 0.40
23 6 0.30
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.84
Consensus pattern (23 bp):
TTGGTTCTTTTTTTTGTTTTTTC
Found at i:44433 original size:27 final size:25
Alignment explanation
Indices: 44382--44448 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
44372 GTGTTTTTGG
*
44382 TTTTTTTT-TTTTTTTTCTTGGTTC
1 TTTTTTTTGTTTTTTTTCTTGCTTC
*
44406 TTTTTTTTGTTTTTTTTACATTTCTTC
1 TTTTTTTTGTTTTTTTT-C-TTGCTTC
*
44433 -TTTTTTTGCTTTTTTT
1 TTTTTTTTGTTTTTTTT
44449 GCAGTAAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 8 0.22
25 8 0.22
26 16 0.43
27 5 0.14
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (25 bp):
TTTTTTTTGTTTTTTTTCTTGCTTC
Done.