Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_412
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: 77357
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:473 original size:46 final size:46
Alignment explanation
Indices: 355--465 Score: 177
Period size: 46 Copynumber: 2.4 Consensus size: 46
345 TCTGAACTCA
* *
355 TTGAGTTGAGCCCGAGTTCACTTATGGATGCGAGCACCCGAGCTCG
1 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCG
* * *
401 CTGAGCTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCG
1 TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCG
447 TTGAGTTGAGTCCGAGTTC
1 TTGAGTTGAGTCCGAGTTC
466 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:2745 original size:138 final size:138
Alignment explanation
Indices: 2324--3012 Score: 941
Period size: 138 Copynumber: 5.1 Consensus size: 138
2314 TAGAAAAATG
* * * *
2324 AATTATATTCTTT-TAGAAAAAA-ATTAATTTCCATATCTTTTATATTTTGACTAAAATTATTTA
1 AATTATATTCTTTCCA-AAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTA
* * * * *
2387 ATGTAAC----TATTTTAATAAATTCAGTAAAATATATACAATTAATAGTTTATATGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
2448 TCATATATT
130 TCATATATT
** **
2457 AATTATATTCTTT-CAAACGGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTA
1 AATTATATTCTTTCCAAA-AAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTA
* * ** *
2521 TTATAACTATTTATATTAATAAATTTAGTAATATATATA-AA-TAATATTTTGTATGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
2584 TCATATATT
130 TCATATATT
* * * * * *
2593 AATTATATTATTTCCAAAAAAATAATAATTTTCATATCTTGTATATTTTGATTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
2658 TATAATTGTGTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
2723 CATAAATT
131 CATATATT
* *
2731 AATTATATTCTTTCCAAAAGAATATTAATTCCCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
*
2796 TATAACTGTTTATATTAATAAATTCGGAAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
2861 CATATATT
131 CATATATT
* * * * *
2869 AATTATATTATTTCGAAAATAATATTAACTTCCATGTCTTTTATA-TTTGACTGAAGTTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* * *
2933 TATAACTGTTTATATTAAAAAATTCGGTAAAATATATAAAATTAATATTTTGCATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
2998 CATATATT
131 CATATATT
3006 -ATTATAT
1 AATTATAT
3013 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:3012 original size:274 final size:272
Alignment explanation
Indices: 2324--3012 Score: 969
Period size: 274 Copynumber: 2.5 Consensus size: 272
2314 TAGAAAAATG
* * * *
2324 AATTATATTCTTTTAGAAAAAA-ATTAATTTCCATATCTTTTATATTTTGACTAAAATTATTTAA
1 AATTATATT-ATTTCGAAAAAATATTAATTTCCATATCTTTTATATTTTGACTGAAATTAATTAA
* * * * *
2388 TGTAAC---TATTTTAATAAATTCAGTAAAATATATACAATTAATAGTTTATATGAATCAAATTC
65 TATAACTGTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
* *
2450 ATATATTAATTATATTCTTTCAAACGGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAAT
130 ATATATTAATTATATTCTTTCAAACAGAATATTAATTCCCATGTCTTTTATATTTTGACCAAAAT
* * * *
2515 TAATTATTATAACTATTTATATTAATAAATTTAGTAATATATATAAATAATATTTTGTATGAATC
195 TAATTAATATAACTATTTATATTAATAAATTCAGAAAAATATATAAATAATATTTTGTATGAATC
2580 AAATTCATATATT
260 AAATTCATATATT
* * * * *
2593 AATTATATTATTTCCAAAAAAATAATAATTTTCATATCTTGTATATTTTGATTGAAATTAATTAA
1 AATTATATTATTT-CGAAAAAATATTAATTTCCATATCTTTTATATTTTGACTGAAATTAATTAA
*
2658 TATAATTGTGTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
65 TATAACTGT-TATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
* **
2723 CATAAATTAATTATATTCTTTCCAAA-AGAATATTAATTCCCATGTCTTTTATATTTTGACTGAA
129 CATATATTAATTATATTCTTT-CAAACAGAATATTAATTCCCATGTCTTTTATATTTTGACCAAA
* *
2787 ATTAATTAATATAACTGTTTATATTAATAAATTCGGAAAAATATATACAATTAATATTTTGTATG
193 ATTAATTAATATAACTATTTATATTAATAAATTCAGAAAAATATATA-AA-TAATATTTTGTATG
2852 AATCAAATTCATATATT
256 AATCAAATTCATATATT
* * *
2869 AATTATATTATTTCGAAAATAATATTAACTTCCATGTCTTTTATA-TTTGACTGAAGTTAATTAA
1 AATTATATTATTTCGAAAA-AATATTAATTTCCATATCTTTTATATTTTGACTGAAATTAATTAA
* * *
2933 TATAACTGTTTATATTAAAAAATTCGGTAAAATATATAAAATTAATATTTTGCATGAATCAAATT
65 TATAACTG-TTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
2998 CATATATT-ATTATAT
129 CATATATTAATTATAT
3013 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:6858 original size:40 final size:40
Alignment explanation
Indices: 6814--6946 Score: 110
Period size: 40 Copynumber: 3.1 Consensus size: 40
6804 ATTAACTAAC
6814 CACATATCAATACCATGTCATTAAACAACTATCAACGCAA
1 CACATATCAATACCATGTCATTAAACAACTATCAACGCAA
* * * * *
6854 CACATAAT-AGTTAACA-GTACACCTTATACATTACCTAATTAAC-TAA
1 CACAT-ATCA-ATACCATGT-CA--TTAAACA--A-CT-ATCAACGCAA
6900 CCACATATCAATACCATGTCATTAAACAACTATCAACGCAA
1 -CACATATCAATACCATGTCATTAAACAACTATCAACGCAA
6941 CACATA
1 CACATA
6947 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:6925 original size:87 final size:87
Alignment explanation
Indices: 6774--6947 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 87
6764 GACCATTCCT
6774 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
1 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
6839 CAACTATCAACGCAACACATAA
66 CAACTATCAACGCAACACATAA
*
6861 TAGTTAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
1 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
6926 CAACTATCAACGCAACACATAA
66 CAACTATCAACGCAACACATAA
6948 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:7995 original size:43 final size:44
Alignment explanation
Indices: 7935--8066 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 44
7925 CACATAAATC
*
7935 ATACAATGCCAACGTCCCAGTCGTGGTCTTACATGTAATCACAT
1 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACAT
* * * *
7979 ATA-GATGCC-ACTGTCCCAAACAG-GATCTTACACGTAATCACAT
1 ATACAATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCACAT
*
8022 A-ACAATGCCAACGTCCCAGACGTGGTATTACATG-AATACACAT
1 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAAT-CACAT
8065 AT
1 AT
8067 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:8386 original size:15 final size:15
Alignment explanation
Indices: 8366--8401 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
8356 GTTCTTGATT
8366 TTCAAATTAAACCCA
1 TTCAAATTAAACCCA
*
8381 TTCAAATTAAACTCA
1 TTCAAATTAAACCCA
8396 TTCAAA
1 TTCAAA
8402 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:12413 original size:51 final size:51
Alignment explanation
Indices: 12330--12467 Score: 165
Period size: 51 Copynumber: 2.7 Consensus size: 51
12320 GATGCCCGAC
*
12330 GGCCTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTCTTCACA-A-AGT
1 GGCCTGCACATAGTACCACACTTGTGA-TCAAAGCTACC-T-TTCACACATAGT
* * *
12381 GGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTCACACATAGT
1 GGCCTGCACATAGTACCACACTTGTGATCAAAGCTACCTTTCACACATAGT
* * *
12432 GGCCTGCACTTAGTACCACACATGTGATCGAAGCTA
1 GGCCTGCACATAGTACCACACTTGTGATCAAAGCTA
12468 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:12468 original size:51 final size:52
Alignment explanation
Indices: 12330--12548 Score: 164
Period size: 51 Copynumber: 4.3 Consensus size: 52
12320 GATGCCCGAC
* * * * * * * *
12330 GGCCTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTC-TTCACAAAGT
1 GGCCTGCACTTAGTACCACACATGTGA-CCAAAGCTATCGTCGTACACATAGT
* * * *
12381 GGCCTTCACATAGTACCACACTTGTGACCAAAGCTATC-T-TTCACACATAGT
1 GGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCGTCGT-ACACATAGT
* * *
12432 GGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCG-GGTACACATAGT
1 GGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCGTCGTACACATAGT
* * * * * * *
12483 AGCCTACACTTAGTACTACACATGCGACCTAA-CTATC-TGGTACACGTAGT
1 GGCCTGCACTTAGTACCACACATGTGACCAAAGCTATCGTCGTACACATAGT
*
12533 AGCCTGCACTTAGTAC
1 GGCCTGCACTTAGTAC
12549 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:12533 original size:50 final size:51
Alignment explanation
Indices: 12373--12610 Score: 192
Period size: 51 Copynumber: 4.7 Consensus size: 51
12363 CTACCTTCTT
* * * * * * * **
12373 CACAAAGTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATC-TTTCA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCTATCGGGT-A
* * * *
12424 CACATAGTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATCGGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCTATCGGGTA
* * *
12475 CACATAGTAGCCTACACTTAGTACTACACATGCGACCTAA-CTATCTGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCTATCGGGTA
* * * * * *****
12525 CACGTAGTAGCCTGCACTTAGTACTATACACGTGACCTAAAACTGTTTTAAA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCT-AAGCTATCGGGTA
* *
12577 CACATTGTAGCCTGCACATAGTACTACACATGTG
1 CACATAGTAGCCTGCACTTAGTACTACACATGTG
12611 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:15943 original size:48 final size:48
Alignment explanation
Indices: 15887--16020 Score: 169
Period size: 48 Copynumber: 2.8 Consensus size: 48
15877 AGATCCCGTA
* * * **
15887 TAAGACCATATCTAGGATATGACATCAGCATCGATATGTGACCCCATG
1 TAAGACCATGTCTAGGACATGGCATTGGCATCGATATGTGACCCCATG
* * * * *
15935 TAAGACCATGTATGGGACATGGCATTGGCACCGTTATGTGATCCCATG
1 TAAGACCATGTCTAGGACATGGCATTGGCATCGATATGTGACCCCATG
*
15983 TAAGATCATGTCTAGGACATGGCATTGGCATCGATATG
1 TAAGACCATGTCTAGGACATGGCATTGGCATCGATATG
16021 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:18983 original size:27 final size:27
Alignment explanation
Indices: 18961--19036 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
18951 TCATCCTATA
*
18961 TTTACTATCCTGATGGACTATCCCGTG
1 TTTACTATCCTGATGGACTATCCCATG
* * * *
18988 TTTACTGTCTTGATGAAATATCCCATG
1 TTTACTATCCTGATGGACTATCCCATG
*
19015 TTTACTATCCCGATGGACTATC
1 TTTACTATCCTGATGGACTATC
19037 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:22678 original size:79 final size:81
Alignment explanation
Indices: 22542--22726 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
22532 TTGAATGATG
* *
22542 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
22606 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
22621 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
22683 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
22701 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
22727 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:22740 original size:40 final size:41
Alignment explanation
Indices: 22542--22726 Score: 222
Period size: 40 Copynumber: 4.6 Consensus size: 41
22532 TTGAATGATG
* * *
22542 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
22582 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
22622 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
22661 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
22702 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
22727 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 35 0.28
40 80 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:22748 original size:79 final size:79
Alignment explanation
Indices: 22595--22759 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
22585 GGACTAAGAT
* * **
22595 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
22660 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
22674 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* * *
22737 TATAT-CTGGTTAAATT
63 TAAATCCGGGTTAAATC
22753 CCGAAGG
1 CCGAAGG
22760 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.66
80 23 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:29348 original size:20 final size:20
Alignment explanation
Indices: 29286--29350 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
29276 TGGTTGAACA
29286 TCCGAACTCGTTGAGTTGAG
1 TCCGAACTCGTTGAGTTGAG
** * *
29306 TCCGAGTTCACTT-A-TGGATG
1 TCCGAACTC-GTTGAGTTGA-G
29326 TCCGAACTCGTTGAGTTGAG
1 TCCGAACTCGTTGAGTTGAG
29346 TCCGA
1 TCCGA
29351 GTTCGTGAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 5 0.15
20 23 0.70
21 5 0.15
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.31
Consensus pattern (20 bp):
TCCGAACTCGTTGAGTTGAG
Found at i:35821 original size:46 final size:46
Alignment explanation
Indices: 35771--35946 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
35761 TGATTGAGCA
35771 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
35817 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
35862 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
35910 -CCTGAGCTCGTTGAGTTGAGTCCAAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
35947 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 60 0.54
47 29 0.26
48 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:35927 original size:93 final size:93
Alignment explanation
Indices: 35768--35939 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
35758 GGATGATTGA
35768 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
*
35833 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCAAGTTCGTGAGATGTAACTAG
*
35861 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGAG
35925 TTGAGTCCAAGTTCG
65 TTGAGTCCAAGTTCG
35940 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCAAGTTCGTGAGATGTAACTAG
Found at i:37298 original size:22 final size:22
Alignment explanation
Indices: 37249--37290 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
37239 GTGGGGGCGT
37249 TACA-CACATAGCCATAAACAG
1 TACAGCACATAGCCATAAACAG
*
37270 TACAGCACATAGCCGTAAACA
1 TACAGCACATAGCCATAAACA
37291 TCGCAGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.29, G:0.12, T:0.14
Consensus pattern (22 bp):
TACAGCACATAGCCATAAACAG
Found at i:37527 original size:22 final size:22
Alignment explanation
Indices: 37493--37557 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
37483 ACAAATATGT
*
37493 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* * *
37515 TTGGCATAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
37537 TTGGCGCAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
37558 AATAATTAGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:37758 original size:41 final size:41
Alignment explanation
Indices: 37701--37821 Score: 161
Period size: 41 Copynumber: 3.0 Consensus size: 41
37691 AAAGCCATCG
* *
37701 GTGGATCCACGGTCGTCAAGCAACCATGTGATCATTAATCA
1 GTGGATCCACGGTCGTCAAGCAACCATGCGATCATCAATCA
* * * *
37742 GTGGATCCACAGTCGTCAAGCAACCATGGGATCCTCAATCG
1 GTGGATCCACGGTCGTCAAGCAACCATGCGATCATCAATCA
* * *
37783 GTGGATTCACGGTCGTCAATCAACCATGCGATCCTCAAT
1 GTGGATCCACGGTCGTCAAGCAACCATGCGATCATCAAT
37822 TTCTTCCTCC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (41 bp):
GTGGATCCACGGTCGTCAAGCAACCATGCGATCATCAATCA
Found at i:38107 original size:27 final size:26
Alignment explanation
Indices: 38077--38289 Score: 160
Period size: 27 Copynumber: 7.9 Consensus size: 26
38067 GGTAAATCTA
38077 CAAACTAAGGGTATTTCGATAATTTTG
1 CAAACTAAGGGTATTTCG-TAATTTTG
* * * *
38104 CAAACCAATGGTATTTTTGTAATTTTT
1 CAAACTAAGGGTA-TTTCGTAATTTTG
* *
38131 TAAAGTTAAGGGTATTTCGTAATTTTG
1 CAAA-CTAAGGGTATTTCGTAATTTTG
* * *
38158 TAAA-TCAGGGGTATTTCTGTAATTTTT
1 CAAACT-AAGGGTATTTC-GTAATTTTG
*
38185 CAAA-TCAAGGGTATTTCAGTAATTTTC
1 CAAACT-AAGGGTATTTC-GTAATTTTG
* * * *
38212 CAAATTAGGGGTATTTTGGTAATTTTA
1 CAAACTAAGGGTA-TTTCGTAATTTTG
* *
38239 CAAACTAGGGGTATTTTGGTAATTTTG
1 CAAACTAAGGGTA-TTTCGTAATTTTG
* *
38266 TAAACCAAGGGTATTTCAGTAATT
1 CAAACTAAGGGTATTTC-GTAATT
38290 CTACCCTACA
Statistics
Matches: 154, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.01
26 13 0.08
27 126 0.82
28 14 0.09
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.42
Consensus pattern (26 bp):
CAAACTAAGGGTATTTCGTAATTTTG
Found at i:38179 original size:54 final size:53
Alignment explanation
Indices: 38077--38289 Score: 212
Period size: 54 Copynumber: 3.9 Consensus size: 53
38067 GGTAAATCTA
* * *
38077 CAAACTAAGGGTATTTCGATAATTTTGCAAACCAATGGTATTTTTGTAATTTTT
1 CAAATTAAGGGTATTTCG-TAATTTTGCAAACCAAGGGTATTTCTGTAATTTTT
* * * *
38131 TAAAGTTAAGGGTATTTCGTAATTTTGTAAATCAGGGGTATTTCTGTAATTTTT
1 CAAA-TTAAGGGTATTTCGTAATTTTGCAAACCAAGGGTATTTCTGTAATTTTT
* * ** * *
38185 CAAATCAAGGGTATTTCAGTAATTTTCCAAATTAGGGGTATTT-TGGTAATTTTA
1 CAAATTAAGGGTATTTC-GTAATTTTGCAAACCAAGGGTATTTCT-GTAATTTTT
* * * * *
38239 CAAACTAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATT
1 CAAATTAAGGGTA-TTTCGTAATTTTGCAAACCAAGGGTATTTCTGTAATT
38290 CTACCCTACA
Statistics
Matches: 131, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
53 13 0.10
54 102 0.78
55 16 0.12
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.42
Consensus pattern (53 bp):
CAAATTAAGGGTATTTCGTAATTTTGCAAACCAAGGGTATTTCTGTAATTTTT
Found at i:38198 original size:81 final size:81
Alignment explanation
Indices: 38075--38289 Score: 242
Period size: 81 Copynumber: 2.7 Consensus size: 81
38065 TTGGTAAATC
* * * ** **
38075 TACAAACTAAGGGTATTTC-GATAATTTTGCAAACCAATGGTATTTTTGTAATTTTTTAAAGTTA
1 TACAAACTAGGGGTATTTCTG-TAATTTTTCAAACCAAGGGTATTTCAGTAATTTTCCAAA-TTA
38139 AGGGTA-TTTCGTAATTT
64 AGGGTATTTTCGTAATTT
** * *
38156 TGTAAA-TCAGGGGTATTTCTGTAATTTTTCAAATCAAGGGTATTTCAGTAATTTTCCAAATTAG
1 TACAAACT-AGGGGTATTTCTGTAATTTTTCAAACCAAGGGTATTTCAGTAATTTTCCAAATTAA
*
38220 GGGTATTTTGGTAATTT
65 GGGTATTTTCGTAATTT
38237 TACAAACTAGGGGTATTT-TGGTAATTTTGT-AAACCAAGGGTATTTCAGTAATT
1 TACAAACTAGGGGTATTTCT-GTAATTTT-TCAAACCAAGGGTATTTCAGTAATT
38290 CTACCCTACA
Statistics
Matches: 113, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
80 10 0.09
81 100 0.88
82 3 0.03
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.42
Consensus pattern (81 bp):
TACAAACTAGGGGTATTTCTGTAATTTTTCAAACCAAGGGTATTTCAGTAATTTTCCAAATTAAG
GGTATTTTCGTAATTT
Found at i:38308 original size:27 final size:27
Alignment explanation
Indices: 38278--38381 Score: 145
Period size: 27 Copynumber: 3.9 Consensus size: 27
38268 AACCAAGGGT
* *
38278 ATTTCAGTAATTCTACCCTACAGTGGC
1 ATTTCAATAATTCTACCCTACAGGGGC
*
38305 ATTTCAATAATTCTATCCTACAGGGGC
1 ATTTCAATAATTCTACCCTACAGGGGC
38332 ATTTCAATAATTCTACCCTACAGGGGC
1 ATTTCAATAATTCTACCCTACAGGGGC
* * * *
38359 ATTTTAGTAAATCTAGCCTACAG
1 ATTTCAATAATTCTACCCTACAG
38382 ATATGAGATT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (27 bp):
ATTTCAATAATTCTACCCTACAGGGGC
Found at i:44791 original size:46 final size:43
Alignment explanation
Indices: 44723--44843 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 43
44713 CCTACAATGG
*
44723 CGATTTTTAGAGAAAAAATATTGTAGTATTCCAATCTTATAGTGAA
1 CGATTTCTAGAGAAAAAATATTGTAGTATTCCAATCTTAT--T-AA
* *
44769 TGATTTCTAGAGAAAAAATA-T-T-GTATT---ATCTCATTAA
1 CGATTTCTAGAGAAAAAATATTGTAGTATTCCAATCTTATTAA
44806 CGATTTCTAGAGAAAAAATATTGTAGTATTCCAATCTT
1 CGATTTCTAGAGAAAAAATATTGTAGTATTCCAATCTT
44844 GAAAATTATT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
37 21 0.33
38 2 0.03
39 1 0.02
40 11 0.17
43 9 0.14
44 1 0.02
45 1 0.02
46 18 0.28
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (43 bp):
CGATTTCTAGAGAAAAAATATTGTAGTATTCCAATCTTATTAA
Found at i:45167 original size:58 final size:58
Alignment explanation
Indices: 45063--45196 Score: 182
Period size: 58 Copynumber: 2.3 Consensus size: 58
45053 TTTAATTCAT
* *
45063 ATAATAATTATATTAAGAATTTTATTAAATTATATATTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATATTATTTTATTAAATTATATTTA
* * * *
45121 GTAATAATTATGTTAA-AATATGATTAAATTATTTATTATTTTTATTAAATTATTTTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATATTA-TTTTATTAAATTATATTTA
45179 ATAATAATCT-TATTAAGA
1 ATAATAAT-TATATTAAGA
45197 TTTAATAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
57 19 0.29
58 44 0.68
59 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (58 bp):
ATAATAATTATATTAAGAATATGATTAAATTATATATTATTTTATTAAATTATATTTA
Found at i:45382 original size:16 final size:16
Alignment explanation
Indices: 45361--45412 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
45351 TAAATTACTG
*
45361 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTAC
** *
45377 ATTACAACTCTATTAA
1 ATTACAGTTCTATTAC
* *
45393 ATTACAGTTCCATTTC
1 ATTACAGTTCTATTAC
45409 ATTA
1 ATTA
45413 TATTGAACTA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTACAGTTCTATTAC
Found at i:48572 original size:21 final size:19
Alignment explanation
Indices: 48548--48588 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
48538 TTGTTAATTG
48548 AAGATTAATGAATAATTAAAT
1 AAGATTAA--AATAATTAAAT
*
48569 AAGATTAAACTAATTAAAT
1 AAGATTAAAATAATTAAAT
48588 A
1 A
48589 TGTTTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (19 bp):
AAGATTAAAATAATTAAAT
Found at i:49685 original size:19 final size:19
Alignment explanation
Indices: 49649--49759 Score: 80
Period size: 19 Copynumber: 5.9 Consensus size: 19
49639 GTACGGGTTT
*
49649 ATGCGCTT-ATGCGCCAGG
1 ATGCGCTTCGTGCGCCAGG
*
49667 ATGCGCTTCGTGCGTCAGG
1 ATGCGCTTCGTGCGCCAGG
* * *
49686 ATGCACTTCCTGTGCCAGG
1 ATGCGCTTCGTGCGCCAGG
* * * *
49705 ATACGCTTTGTGCACTAGG
1 ATGCGCTTCGTGCGCCAGG
* * * *
49724 ATGCACTTTGTGCGACAAG
1 ATGCGCTTCGTGCGCCAGG
* *
49743 ATGCACTTCATGCGCCA
1 ATGCGCTTCGTGCGCCA
49760 ATATTCACTA
Statistics
Matches: 70, Mismatches: 22, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
18 8 0.11
19 62 0.89
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.26
Consensus pattern (19 bp):
ATGCGCTTCGTGCGCCAGG
Found at i:51512 original size:21 final size:21
Alignment explanation
Indices: 51486--51541 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
51476 TGTGGTCCAA
51486 GGGACACGCCCGTGTGACCCT
1 GGGACACGCCCGTGTGACCCT
*
51507 GGGACACGTCCGTGTGACCCT
1 GGGACACGCCCGTGTGACCCT
51528 GGGACACGCCCGTG
1 GGGACACGCCCGTG
51542 CTGGAGGCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.14, C:0.36, G:0.36, T:0.14
Consensus pattern (21 bp):
GGGACACGCCCGTGTGACCCT
Found at i:51735 original size:42 final size:42
Alignment explanation
Indices: 51657--51737 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
51647 GTGCAGGTTT
* * * *
51657 CACACGGCTAAGACACATGCCCGTGTTGTAGGCCGTGTGGCA
1 CACACGGCTAAGACACAAGCCCATGTTCTAGCCCGTGTGGCA
*
51699 CACACGGCTGAGACACAAGCCCATGTCTCT-GCCCGTGTG
1 CACACGGCTAAGACACAAGCCCATGT-TCTAGCCCGTGTG
51738 CTCAATTCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.21, C:0.32, G:0.28, T:0.19
Consensus pattern (42 bp):
CACACGGCTAAGACACAAGCCCATGTTCTAGCCCGTGTGGCA
Found at i:56645 original size:46 final size:46
Alignment explanation
Indices: 56578--56933 Score: 471
Period size: 46 Copynumber: 7.7 Consensus size: 46
56568 GCTTTCTGAA
* * *
56578 ATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
56624 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** ** *
56670 GGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAATGTGAT
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * *
56717 ATGAAATGTGTAAGATCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
56763 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
56809 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
56855 GGGAAAATGAATAAGACCATGGTTGGAAGATACCATGGCAACATGAC
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
56902 A-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 ATG-AAATGAATAAGACCATGGTTGAAAGATAC
56934 TATGACATTA
Statistics
Matches: 275, Mismatches: 33, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
46 194 0.71
47 81 0.29
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:56698 original size:93 final size:93
Alignment explanation
Indices: 56581--56933 Score: 539
Period size: 93 Copynumber: 3.8 Consensus size: 93
56571 TTCTGAAATG
* *
56581 AAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAGTAAGACCATGGT
1 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAGACCATGGT
56646 TGAAAGATACCATGGCAACATGACGGGA
66 TGAAAGATACCATGGCAACATGACGGGA
** * * *
56674 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAATGTGATATGAAATGTGTAAGATCATGGT
1 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAGACCATGGT
* ***
56739 TGAAAGATACCATGGCAACGTGATATG-
66 TGAAAGATACCATGGCAACATGACGGGA
56766 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAGACCATGGT
1 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAGACCATGGT
56831 TGAAAGATACCATGGCAACATGACGGGA
66 TGAAAGATACCATGGCAACATGACGGGA
* * * * *
56859 AAATGAATAAGACCATGGTTGGAAGATACCATGGCAACATGACA-GAAAACGAGTAAAACCATAG
1 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAATGAGTAAGACCATGG
56923 TTGAAAGATAC
65 TTGAAAGATAC
56934 TATGACATTA
Statistics
Matches: 235, Mismatches: 23, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
92 84 0.36
93 151 0.64
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (93 bp):
AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAGACCATGGT
TGAAAGATACCATGGCAACATGACGGGA
Found at i:56928 original size:185 final size:185
Alignment explanation
Indices: 56578--56933 Score: 597
Period size: 185 Copynumber: 1.9 Consensus size: 185
56568 GCTTTCTGAA
*
56578 ATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAGTAAGACCAT
1 ATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAGACCAT
56643 GGTTGAAAGATACCATGGCAACATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGG
66 GGTTGAAAGATACCATGGCAACATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGG
** * * * * * *
56708 CAATGTGATATGAAATGTGTAAGATCATGGTTGAAAGATACCATGGCAACGTGAT
131 CAACATGACATGAAACGAGTAAAACCATAGTTGAAAGATACCATGGCAACGTGAT
*
56763 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAGACCAT
1 ATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAGACCAT
*
56828 GGTTGAAAGATACCATGGCAACATGACGGGAAAATGAATAAGACCATGGTTGGAAGATACCATGG
66 GGTTGAAAGATACCATGGCAACATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGG
56893 CAACATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
131 CAACATGACATG-AAACGAGTAAAACCATAGTTGAAAGATAC
56934 TATGACATTA
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
184 1 0.01
185 158 0.99
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (185 bp):
ATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGACATGAAATGAGTAAGACCAT
GGTTGAAAGATACCATGGCAACATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGG
CAACATGACATGAAACGAGTAAAACCATAGTTGAAAGATACCATGGCAACGTGAT
Found at i:61136 original size:35 final size:35
Alignment explanation
Indices: 61097--61167 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
61087 GAGTGAGCTT
61097 TTTCACTCTTAAGCAACTCAAGTTTCTTTCCATGA
1 TTTCACTCTTAAGCAACTCAAGTTTCTTTCCATGA
61132 TTTCACTCTTAAGCAACTCAAGTTTCTTTCCATGA
1 TTTCACTCTTAAGCAACTCAAGTTTCTTTCCATGA
61167 T
1 T
61168 CATCATGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.41
Consensus pattern (35 bp):
TTTCACTCTTAAGCAACTCAAGTTTCTTTCCATGA
Found at i:70883 original size:49 final size:47
Alignment explanation
Indices: 70806--70940 Score: 146
Period size: 49 Copynumber: 2.8 Consensus size: 47
70796 AGAAATTTCA
* * *
70806 GCACTATGTGTGCGAGGTTATGCGGCACTATGTGTGCAA-AAACTACGTG
1 GCACTATGTGTGCGAGATTA-ACAGCACTATGTGTGCAAGAAA--ACGTG
* *
70855 GCACTATGTGTGCGAGATTACATAGCACTATGTGTGCAAGGAAACGTG
1 GCACTATGTGTGCGAGATTA-ACAGCACTATGTGTGCAAGAAAACGTG
* *
70903 GCACTATGTGTGCGAATGAGTAAGAGCACTATGTGTGC
1 GCACTATGTGTGCG-A-GATTAACAGCACTATGTGTGC
70941 GGACCTTTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
48 19 0.25
49 50 0.67
50 6 0.08
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (47 bp):
GCACTATGTGTGCGAGATTAACAGCACTATGTGTGCAAGAAAACGTG
Found at i:70887 original size:24 final size:24
Alignment explanation
Indices: 70805--70941 Score: 98
Period size: 24 Copynumber: 5.6 Consensus size: 24
70795 AAGAAATTTC
* * *
70805 AGCACTATGTGTGCGAGGTTATGC
1 AGCACTATGTGTGCGAGATTACGT
* * * *
70829 GGCACTATGTGTGCAAAAACTACGT
1 AGCACTATGTGTGC-GAGATTACGT
* *
70854 GGCACTATGTGTGCGAGATTACAT
1 AGCACTATGTGTGCGAGATTACGT
* *
70878 AGCACTATGTGTGCAAGGA-AACGT
1 AGCACTATGTGTGCGA-GATTACGT
* * *
70902 GGCACTATGTGTGCGAATGAGTAAG-
1 AGCACTATGTGTGCG-A-GATTACGT
70927 AGCACTATGTGTGCG
1 AGCACTATGTGTGCG
70942 GACCTTTAAA
Statistics
Matches: 88, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
24 49 0.56
25 37 0.42
26 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.26
Consensus pattern (24 bp):
AGCACTATGTGTGCGAGATTACGT
Found at i:72467 original size:15 final size:15
Alignment explanation
Indices: 72444--72482 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
72434 TATGATATTG
*
72444 TATCTTGGATTTCTT
1 TATCTTGGATTTCTC
*
72459 TATCATGGATTTCTC
1 TATCTTGGATTTCTC
72474 TATCTTGGA
1 TATCTTGGA
72483 CGTCTTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Done.