Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000696.1 Hibiscus syriacus cultivar Beakdansim tig00001356_pilon, whole genome shotgun sequence
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: 77291
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:418 original size:14 final size:14
Alignment explanation
Indices: 395--438 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
385 ATTATGCTTG
*
395 AAGAAGAAAAAGAA
1 AAGAAAAAAAAGAA
*
409 AAG-AAAAAAATAA
1 AAGAAAAAAAAGAA
422 AAGAAAAAAAAAGAA
1 AAG-AAAAAAAAGAA
437 AA
1 AA
439 ATGATGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 11 0.44
14 3 0.12
15 11 0.44
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:423 original size:13 final size:13
Alignment explanation
Indices: 395--431 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
385 ATTATGCTTG
395 AAGAAGAAAAAGAA
1 AAGAA-AAAAAGAA
*
409 AAGAAAAAAATAA
1 AAGAAAAAAAGAA
422 AAGAAAAAAA
1 AAGAAAAAAA
432 AAGAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:829 original size:18 final size:18
Alignment explanation
Indices: 794--864 Score: 78
Period size: 17 Copynumber: 4.1 Consensus size: 18
784 CAAGTTTATC
794 TTTTCG-AATTC-ATTTA
1 TTTTCGAAATTCAATTTA
*
810 TTTTCGAAATTCAATATA
1 TTTTCGAAATTCAATTTA
* *
828 -TTTCCAAAGTCCAATTTA
1 TTTTCGAAA-TTCAATTTA
846 TTTT-GAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
863 TT
1 TT
865 CTTGCAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.13
17 22 0.49
18 14 0.31
19 3 0.07
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:2358 original size:111 final size:110
Alignment explanation
Indices: 2182--2607 Score: 452
Period size: 110 Copynumber: 3.8 Consensus size: 110
2172 TACATTCAAT
* * *
2182 GATCAATATTTCTAGGTAGAGTTCATAATGAGAAGAAGTCATCTGAAGAAGGA-AGAGAAATTCA
1 GATCAACATTTCCA-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGA-AGAAATTCA
* *
2246 TAATGAGAAGAATTTGTTCAACCTTTTACTTGAATTCATC-CTTCGATA
64 TAATGAGAAGAACTTGTTCAACCTTTT-CATGAATTCATCAC-TCGATA
*
2294 GATCAACATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAGGAAATTCATA
1 GATCAACATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCATA
* * * * *
2359 ATGAGAAGAATTTGTTTAA-CTTTTCGCTGATTTCATCACTCGATG
66 ATGAGAAGAACTTGTTCAACCTTTTC-ATGAATTCATCACTCGATA
* * * * * *
2404 GAT-AACTTTTACAG-AGAAAGTTCATAATGAGAAGTACTTATCGGAA-AAGGAAGAAGAAGTTC
1 GATCAACATTTCCAGTAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAATTC
**
2466 ATAATGAGAAGAACTTGTTCAACCTTTTGCATG-ATTCTATCACAGAAGGAGATA
63 ATAATGAGAAGAACTTGTTCAACCTTTT-CATGAATTC-ATCAC-----TCGATA
* * * * *
2520 GATCAACATTTTCAGAAGTGTTCATAATGAGAAGAATTCATCTGAAGAAGGAGAAGAAGTTCATA
1 GATCAACATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCATA
2585 ATGAGAAGAACTTGTTCAACCTT
66 ATGAGAAGAACTTGTTCAACCTT
2608 GCCTTAATTC
Statistics
Matches: 268, Mismatches: 29, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
108 2 0.01
109 14 0.05
110 79 0.29
111 78 0.29
112 14 0.05
116 66 0.25
117 13 0.05
118 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (110 bp):
GATCAACATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAATTCATA
ATGAGAAGAACTTGTTCAACCTTTTCATGAATTCATCACTCGATA
Found at i:2591 original size:23 final size:22
Alignment explanation
Indices: 2548--2592 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2538 TGTTCATAAT
*
2548 GAGAAGAATTCATCTGAAGAAG
1 GAGAAGAATTCATATGAAGAAG
2570 GAGAAGAAGTTCATAATG-AGAAG
1 GAGAAGAA-TTCAT-ATGAAGAAG
2593 AACTTGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 10 0.50
24 2 0.10
ACGTcount: A:0.47, C:0.07, G:0.29, T:0.18
Consensus pattern (22 bp):
GAGAAGAATTCATATGAAGAAG
Found at i:2969 original size:5 final size:5
Alignment explanation
Indices: 2959--3015 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
2949 CATTTGTTAT
* * * *
2959 TATTA TATTA TGTTA T-TTA TTACTA TATTA TTTTA TAATTT TATTA TATTA
1 TATTA TATTA TATTA TATTA -TATTA TATTA TATTA T-ATTA TATTA TATTA
3010 TATTA T
1 TATTA T
3016 TAATAAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
4 3 0.07
5 34 0.81
6 5 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (5 bp):
TATTA
Found at i:7721 original size:24 final size:24
Alignment explanation
Indices: 7692--7755 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
7682 AAAACAGGAG
*
7692 CTCGATTGAAGCTCGAGACTCGAT
1 CTCGATTGAAGCTCGAGAATCGAT
7716 CTCGATTGAAGCTCGAGAATCGAT
1 CTCGATTGAAGCTCGAGAATCGAT
7740 CTCGATTGAAGCTCGA
1 CTCGATTGAAGCTCGA
7756 TTTTGAGCTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (24 bp):
CTCGATTGAAGCTCGAGAATCGAT
Found at i:7799 original size:17 final size:17
Alignment explanation
Indices: 7774--7810 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
7764 TCAATTCAAG
7774 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
*
7791 CTCGGTTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
7808 CTC
1 CTC
7811 AAACTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:7805 original size:11 final size:11
Alignment explanation
Indices: 7740--7789 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
7730 GAGAATCGAT
*
7740 CTCGATTGAAG
1 CTCGATTCAAG
**
7751 CTCGATTTTGAG
1 CTCGA-TTCAAG
*
7763 CTCAATTCAAG
1 CTCGATTCAAG
7774 CTCGATTCAAG
1 CTCGATTCAAG
7785 CTCGA
1 CTCGA
7790 ACTCGGTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 24 0.75
12 8 0.25
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (11 bp):
CTCGATTCAAG
Found at i:8068 original size:37 final size:36
Alignment explanation
Indices: 8018--8090 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 36
8008 GAAAGTTTAC
*
8018 AAAATATGACAACACATCTAAATTTATAAAAAGATGA
1 AAAATATGACAACACATCCAAATTTAT-AAAAGATGA
* *
8055 AAAATATGACAACATATCCAAATTTATATAAGATGA
1 AAAATATGACAACACATCCAAATTTATAAAAGATGA
8091 CACTATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 8 0.24
37 25 0.76
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (36 bp):
AAAATATGACAACACATCCAAATTTATAAAAGATGA
Found at i:8236 original size:30 final size:31
Alignment explanation
Indices: 8181--8241 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
8171 CCAGTTAAGC
8181 TTACTTACAAAAGATGGAAGCAACATGTCAAGT
1 TTACTTACAAAAGAT-G-AGCAACATGTCAAGT
*
8214 TTACTTACAAAAGAT-TGCAACATGTCAA
1 TTACTTACAAAAGATGAGCAACATGTCAA
8242 ATTAAGTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.44
33 15 0.56
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (31 bp):
TTACTTACAAAAGATGAGCAACATGTCAAGT
Found at i:10535 original size:7 final size:7
Alignment explanation
Indices: 10523--10576 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
10513 AATCATATTA
10523 AGGGTTT
1 AGGGTTT
10530 AGGGTTT
1 AGGGTTT
* *
10537 AAGATTT
1 AGGGTTT
*
10544 ATGGTTT
1 AGGGTTT
*
10551 ATGGTTT
1 AGGGTTT
* *
10558 AGAGTAT
1 AGGGTTT
10565 AGGGTTT
1 AGGGTTT
10572 AGGGT
1 AGGGT
10577 GTAATCTAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:10551 original size:21 final size:21
Alignment explanation
Indices: 10523--10576 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
10513 AATCATATTA
*
10523 AGGGTTTAGGGTTTA-AGATTT
1 AGGGTTTAGGGTTTAGAG-TAT
* *
10544 ATGGTTTATGGTTTAGAGTAT
1 AGGGTTTAGGGTTTAGAGTAT
10565 AGGGTTTAGGGT
1 AGGGTTTAGGGT
10577 GTAATCTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (21 bp):
AGGGTTTAGGGTTTAGAGTAT
Found at i:11765 original size:41 final size:43
Alignment explanation
Indices: 11686--11766 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
11676 AAGTTGAAAA
* * *
11686 ATATTTATATATTTTCTTTAAAAAATTTAAATTCATAAAATTT
1 ATATATATATATTTTCTTTAAAAAATTGAAAGTCATAAAATTT
* *
11729 ATATATATATATTTT-TTTACAAAATTGACAGT-ATAAAA
1 ATATATATATATTTTCTTTAAAAAATTGAAAGTCATAAAA
11767 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 6 0.18
42 13 0.39
43 14 0.42
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (43 bp):
ATATATATATATTTTCTTTAAAAAATTGAAAGTCATAAAATTT
Found at i:23926 original size:54 final size:54
Alignment explanation
Indices: 23860--24087 Score: 325
Period size: 54 Copynumber: 4.2 Consensus size: 54
23850 TTATGTGTTT
*
23860 TGCACA-TATAGTGTCGAAACGATTATTCATCCACATAGGATAAATTCCGTGAAA
1 TGCACACT-TAGTGTCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAA
* *
23914 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGTCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
23968 TGTACAATTAGTG-CTGAAACGATTATTCATCAACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGTC-GAAACGATTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
24022 TGCACACTTAATGTCGAAACGGTTATTTATCCATATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGTCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAA
*
24076 TGCACACGTAGT
1 TGCACACTTAGT
24088 ACTGATTTGG
Statistics
Matches: 155, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 152 0.98
55 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (54 bp):
TGCACACTTAGTGTCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:25240 original size:30 final size:30
Alignment explanation
Indices: 25204--25298 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
25194 TTTAAACCAC
25204 TAATCCAAATCATTCTCATCATTTATCATT
1 TAATCCAAATCATTCTCATCATTTATCATT
*
25234 TTATCCAAATCATTCTCATCATTTATCATT
1 TAATCCAAATCATTCTCATCATTTATCATT
*
25264 TAATCCAAATCATTCTCATCATCTATCATT
1 TAATCCAAATCATTCTCATCATTTATCATT
25294 TAATC
1 TAATC
25299 GAATAAATCC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (30 bp):
TAATCCAAATCATTCTCATCATTTATCATT
Found at i:25312 original size:30 final size:30
Alignment explanation
Indices: 25204--25312 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 30
25194 TTTAAACCAC
* * *
25204 TAATCCAAATCATTCTCATCATTTATCATT
1 TAATCCAAATAATCCTCATCATCTATCATT
* * * *
25234 TTATCCAAATCATTCTCATCATTTATCATT
1 TAATCCAAATAATCCTCATCATCTATCATT
* *
25264 TAATCCAAATCATTCTCATCATCTATCATT
1 TAATCCAAATAATCCTCATCATCTATCATT
*
25294 TAAT-CGAATAAATCCTCAT
1 TAATCCAAAT-AATCCTCAT
25313 ATTTTTACAT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
29 4 0.06
30 68 0.94
ACGTcount: A:0.34, C:0.24, G:0.01, T:0.41
Consensus pattern (30 bp):
TAATCCAAATAATCCTCATCATCTATCATT
Found at i:25312 original size:60 final size:59
Alignment explanation
Indices: 25204--25316 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 59
25194 TTTAAACCAC
* * * *
25204 TAATCCAAATCATTCTCATCATTTATCATTTTATCCAAATCATTCTCATCATTTATCATT
1 TAATCCAAATCATTCTCATCATCTATCATTTAATCCAAATAATCCTCAT-ATTTATCATT
*
25264 TAATCCAAATCATTCTCATCATCTATCATTTAAT-CGAATAAATCCTCATATTT
1 TAATCCAAATCATTCTCATCATCTATCATTTAATCCAAAT-AATCCTCATATTT
25317 TTACATCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
59 8 0.17
60 39 0.83
ACGTcount: A:0.34, C:0.23, G:0.01, T:0.42
Consensus pattern (59 bp):
TAATCCAAATCATTCTCATCATCTATCATTTAATCCAAATAATCCTCATATTTATCATT
Found at i:30951 original size:40 final size:40
Alignment explanation
Indices: 30891--30975 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 40
30881 ATGTGAAATT
*
30891 TGTCCCGAAGGACTTATGTATGTCCTGAAGGACCTCTGTA
1 TGTCCCGAAGGACCTATGTATGTCCTGAAGGACCTCTGTA
* *
30931 TGTCCCGAAGGACCTCTGTATGTTCTGAAGGACCTCTGTA
1 TGTCCCGAAGGACCTATGTATGTCCTGAAGGACCTCTGTA
30971 TGTCC
1 TGTCC
30976 TAAAAGACCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (40 bp):
TGTCCCGAAGGACCTATGTATGTCCTGAAGGACCTCTGTA
Found at i:30985 original size:20 final size:20
Alignment explanation
Indices: 30891--30976 Score: 127
Period size: 20 Copynumber: 4.3 Consensus size: 20
30881 ATGTGAAATT
* * *
30891 TGTCCCGAAGGACTTATGTA
1 TGTCCTGAAGGACCTCTGTA
30911 TGTCCTGAAGGACCTCTGTA
1 TGTCCTGAAGGACCTCTGTA
*
30931 TGTCCCGAAGGACCTCTGTA
1 TGTCCTGAAGGACCTCTGTA
*
30951 TGTTCTGAAGGACCTCTGTA
1 TGTCCTGAAGGACCTCTGTA
30971 TGTCCT
1 TGTCCT
30977 AAAAGACCTA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
TGTCCTGAAGGACCTCTGTA
Found at i:30985 original size:40 final size:40
Alignment explanation
Indices: 30907--30985 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
30897 GAAGGACTTA
* *
30907 TGTATGTCCTGAAGGACCTCTGTATGTCCCGAAGGACCTC
1 TGTATGTCCTGAAGGACCTCTGTATGTCCCAAAAGACCTC
* *
30947 TGTATGTTCTGAAGGACCTCTGTATGTCCTAAAAGACCT
1 TGTATGTCCTGAAGGACCTCTGTATGTCCCAAAAGACCT
30986 ATGAACTCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (40 bp):
TGTATGTCCTGAAGGACCTCTGTATGTCCCAAAAGACCTC
Found at i:34641 original size:11 final size:11
Alignment explanation
Indices: 34625--34659 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
34615 ATGTAACATC
34625 CCAACCCGGAT
1 CCAACCCGGAT
34636 CCAACCCGGAT
1 CCAACCCGGAT
*
34647 CCGACCCGGAT
1 CCAACCCGGAT
34658 CC
1 CC
34660 GAGTCCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.23, C:0.49, G:0.20, T:0.09
Consensus pattern (11 bp):
CCAACCCGGAT
Found at i:35347 original size:20 final size:20
Alignment explanation
Indices: 35322--35359 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35312 ATGTGAAATT
*
35322 TGTCCCAAATGACCTATGTA
1 TGTCCCAAAGGACCTATGTA
*
35342 TGTCCCGAAGGACCTATG
1 TGTCCCAAAGGACCTATG
35360 AACCCTCGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
TGTCCCAAAGGACCTATGTA
Found at i:37334 original size:54 final size:54
Alignment explanation
Indices: 37276--37787 Score: 722
Period size: 54 Copynumber: 9.5 Consensus size: 54
37266 TTAACATATT
*** * *
37276 ATGAATTCCGTGTTTTGCACACATAGTGCCGAAACGGTTATTCATTCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * * *
37330 ATGAACTCCTTGAAATGCACACTTAGTGCCAAAATGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * ** * *
37384 ATGAATTCTGTGAAATGAACACTTAGTGTTGAAACAGTTATTCATCTACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
** * *
37438 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAATTATTCATCCACACATG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* *
37492 ATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGCTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
37546 ATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGATTTTTCATCCAC--AGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
*
37598 ATGAATTCCATGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * * *
37652 ATGAATTCCGTGAAATACACACTTAGTGTCGAAATGATTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
37706 ATGAATTCCGTGAAATGCACATTTAGTGTCGAAACGATTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
37760 ATGAATTCCGTGAAATGCACACTTAGTG
1 ATGAATTCCGTGAAATGCACACTTAGTG
37788 TCGATTTGGT
Statistics
Matches: 405, Mismatches: 51, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
52 48 0.12
54 357 0.88
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (54 bp):
ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
Found at i:37694 original size:214 final size:215
Alignment explanation
Indices: 37293--37791 Score: 739
Period size: 214 Copynumber: 2.3 Consensus size: 215
37283 CCGTGTTTTG
* * * *
37293 CACACATAGTGCCGAAACGGTTATTCATTCACATAGGATGAACTCCTTGAAATGCACACTTAGTG
1 CACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
* * * * ** **
37358 CCAAAATGGTTATTCATCCACATAGGATGAATTCTGTGAAATGAACACTTAGTGTTGAAACAGTT
66 TCGAAACGATTATTCATCCACA-AGGATGAATTCCATGAAATGAACACTTAGTGCCGAAACAGTT
* *
37423 ATTCATCTACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACAATTATTCATCCACA
130 ATTCATCCACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACAATTATTCATCCACA
*
37488 CATGATGAATTCCGTGAAATA
195 CAGGATGAATTCCGTGAAATA
*
37509 CACACTTAGTGCCGAAACGGCTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
1 CACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
* * *
37574 TCGAAACGATTTTTCATCCAC-AGGATGAATTCCATGAAATGCACACTTAGTGCCGAAACGGTTA
66 TCGAAACGATTATTCATCCACAAGGATGAATTCCATGAAATGAACACTTAGTGCCGAAACAGTTA
* ** *
37638 TTCATCCACATAGGATGAATTCCGTGAAATACACACTTAGTGTCGAAATGATTATTCATCCACAT
131 TTCATCCACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACAATTATTCATCCACAC
*
37703 AGGATGAATTCCGTGAAATG
196 AGGATGAATTCCGTGAAATA
* * *
37723 CACATTTAGTGTCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
1 CACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
37788 TCGA
66 TCGA
37792 TTTGGTAATC
Statistics
Matches: 255, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
214 179 0.70
216 76 0.30
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (215 bp):
CACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
TCGAAACGATTATTCATCCACAAGGATGAATTCCATGAAATGAACACTTAGTGCCGAAACAGTTA
TTCATCCACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACAATTATTCATCCACAC
AGGATGAATTCCGTGAAATA
Found at i:38153 original size:22 final size:21
Alignment explanation
Indices: 38116--38184 Score: 90
Period size: 22 Copynumber: 3.4 Consensus size: 21
38106 GCTCTTCAGA
38116 ATCGATAC-ACATACTATGGT
1 ATCGATACTACATACTATGGT
38136 ATCGATACTACCATACTATGGT
1 ATCGATACTA-CATACTATGGT
*
38158 ACCGATACT--ATACTATGGT
1 ATCGATACTACATACTATGGT
*
38177 ATTGATAC
1 ATCGATAC
38185 ATTACCTTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
19 16 0.36
20 8 0.18
21 1 0.02
22 19 0.43
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (21 bp):
ATCGATACTACATACTATGGT
Found at i:40303 original size:227 final size:238
Alignment explanation
Indices: 40014--40511 Score: 581
Period size: 254 Copynumber: 2.1 Consensus size: 238
40004 TATATCCGGG
* *
40014 TCGGGTTCGGATCGGGTGAAACTTTATTTTGGTTGGGTCAGGTCGGTTTTTTTAAGTGTGATATT
1 TCGGG-TCGGGTCGGGTGAAACTTTATTTTGGTTGGGTCAGGTCGGGTTTTTTAAGTGTGATATT
* * * * *
40079 C-GGG-T-CG-G-G-TC-GA-GTTCGGGTTTAGGGT-GAAAAA-T-ACCCGACCCGAAAATATAT
65 CGGGGTTAAGTGTGATCGGAGGTTCGGGTTTAGGGTAAAAAAATTAACCCGACCCAAAAAAAAAT
40133 ATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTAAATATA-ATTTTTTTCA
130 ATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTAAATATATA-TTTTTTCA
* *
40197 ATTAAGTCACTACTTTTATTGAATAAAACTAATTTTTTTATTATT
194 ATTAAGTCAATACTTTTATTGAATAAAAATAATTTTTTTATTATT
40242 TCGGGTCGGGTCGGGTGAAACTTTATTTT-GTTCGGGTCAGGTCGGGTTTTTTAAGTGTGATATT
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTT-GGGTCAGGTCGGGTTTTTTAAGTGTGATATT
* *
40306 CGGGTTGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAATTAGACT
65 C--G--GGG-----TTAAGTGTG--A-TC-GG--AGGTTCGGGTTTAGGGTAAAAAAATTA-ACC
**
40371 CGACCCAAAAAAAAATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTCT
114 CGACCCAAAAAAAAATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTAA
**
40436 ATATATATTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTATT
179 ATATATATTTTTTCAATTAAGTCAATACTTTTATTGAATAAAAATAATTTTTTTATTATT
* *
40496 TTGTGTCGGGTCGGGT
1 TCGGGTCGGGTCGGGT
40512 CAGGTTTCTA
Statistics
Matches: 224, Mismatches: 17, Indels: 32
0.82 0.06 0.12
Matches are distributed among these distances:
226 3 0.01
227 54 0.24
228 5 0.02
232 3 0.01
238 1 0.00
239 1 0.00
240 1 0.00
241 1 0.00
245 2 0.01
247 1 0.00
250 15 0.07
251 5 0.02
252 1 0.00
254 130 0.58
255 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (238 bp):
TCGGGTCGGGTCGGGTGAAACTTTATTTTGGTTGGGTCAGGTCGGGTTTTTTAAGTGTGATATTC
GGGGTTAAGTGTGATCGGAGGTTCGGGTTTAGGGTAAAAAAATTAACCCGACCCAAAAAAAAATA
TAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTAAATATATATTTTTTCAAT
TAAGTCAATACTTTTATTGAATAAAAATAATTTTTTTATTATT
Found at i:40319 original size:28 final size:28
Alignment explanation
Indices: 40281--40344 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
40271 GTTCGGGTCA
40281 GGTCGGG-TTTTTTAAGTGTGATATTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCG
*
40308 GGTTGGGTTTTTTTAAGTGTGATATTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCG
40336 GGTCGGGTT
1 GGTCGGGTT
40345 CGGGTTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 6 0.18
28 28 0.82
ACGTcount: A:0.12, C:0.06, G:0.36, T:0.45
Consensus pattern (28 bp):
GGTCGGGTTTTTTTAAGTGTGATATTCG
Found at i:42067 original size:50 final size:49
Alignment explanation
Indices: 41948--42067 Score: 132
Period size: 50 Copynumber: 2.4 Consensus size: 49
41938 GTAAAGCGAA
* * *
41948 CCCCCTGAACCGCGTTATACGTTGATTTCGTGCCACGTGGGTATAGCGCG
1 CCCCCTGAACCGC-ATATACGGTGATTTCGTGCCACGCGGGTATAGCGCG
* * ** *
41998 TCCACTGCCCCGCGATATACGGTGATTTGGTGCCACGCGGGTATAGCGCG
1 CCCCCTGAACCGC-ATATACGGTGATTTCGTGCCACGCGGGTATAGCGCG
*
42048 CCCCCTGATCCGCACTATAC
1 CCCCCTGAACCGCA-TATAC
42068 CTGGGTATCT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
49 1 0.02
50 56 0.98
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (49 bp):
CCCCCTGAACCGCATATACGGTGATTTCGTGCCACGCGGGTATAGCGCG
Found at i:42228 original size:20 final size:19
Alignment explanation
Indices: 42188--42228 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
42178 TTTTATCACA
* *
42188 CTAAATTCTCTCATATTCT
1 CTAAATTCTCTCAAATACT
42207 CTAAATTTCTCTCAAATACT
1 CTAAA-TTCTCTCAAATACT
42227 CT
1 CT
42229 CTCTTTAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (19 bp):
CTAAATTCTCTCAAATACT
Found at i:42565 original size:111 final size:111
Alignment explanation
Indices: 42371--42703 Score: 630
Period size: 111 Copynumber: 3.0 Consensus size: 111
42361 TGGAAATCAT
* *
42371 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTGATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
42436 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
42482 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
42547 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
42593 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
42658 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
42704 TTTTTGTAAT
Statistics
Matches: 218, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 218 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:44617 original size:9 final size:9
Alignment explanation
Indices: 44605--44648 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
44595 CGACGACGTT
44605 GATGACGAC
1 GATGACGAC
*
44614 GATGACGAT
1 GATGACGAC
*
44623 GGTGACGAC
1 GATGACGAC
*
44632 GACGACGAC
1 GATGACGAC
*
44641 GACGACGA
1 GATGACGA
44649 TGACAGCGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.36, T:0.09
Consensus pattern (9 bp):
GATGACGAC
Found at i:44620 original size:18 final size:18
Alignment explanation
Indices: 44593--44639 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
44583 TGCTCAGGAT
*
44593 GACGACGACGTTGATGAC
1 GACGACGACGATGATGAC
* *
44611 GACGATGACGATGGTGAC
1 GACGACGACGATGATGAC
44629 GACGACGACGA
1 GACGACGACGA
44640 CGACGACGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.21, G:0.36, T:0.13
Consensus pattern (18 bp):
GACGACGACGATGATGAC
Found at i:44904 original size:35 final size:33
Alignment explanation
Indices: 44865--44949 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
44855 ATATTTTAGT
44865 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
44900 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
44935 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
44950 TGAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:50395 original size:35 final size:35
Alignment explanation
Indices: 50348--50433 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
50338 AAAACAATCA
* * *
50348 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
50383 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
50418 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
50434 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:50427 original size:21 final size:21
Alignment explanation
Indices: 50402--50444 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
50392 TTCTAAACCC
50402 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
50423 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
50444 T
1 T
50445 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:50598 original size:16 final size:18
Alignment explanation
Indices: 50566--50599 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
50556 TATTAATGTA
50566 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
50584 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
50600 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:51272 original size:130 final size:130
Alignment explanation
Indices: 51069--51316 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
51059 AATTTTCTTC
* * *
51069 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAAAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAAAT
*
51134 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGTATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGTATATATAAA
* * * * *
51199 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAAAT
51264 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
51317 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAAAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGTATATATAAA
Found at i:51928 original size:31 final size:29
Alignment explanation
Indices: 51893--51962 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
51883 TGTGGTTTAA
51893 GTTGGGGGA-TCATATTGCAAACGGATTAAAT
1 GTTGGGGGACT-ATATTGC-AA-GGATTAAAT
* **
51924 GTTGGGGGACTGTATTGCAAGTTTTAAAT
1 GTTGGGGGACTATATTGCAAGGATTAAAT
51953 GTTGGGGGAC
1 GTTGGGGGAC
51963 CTAAATGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.49
30 2 0.06
31 15 0.43
32 1 0.03
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.31
Consensus pattern (29 bp):
GTTGGGGGACTATATTGCAAGGATTAAAT
Found at i:51971 original size:29 final size:29
Alignment explanation
Indices: 51918--51973 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
51908 TGCAAACGGA
* *
51918 TTAAATGTTGGGGGACTGTATTGCAAGTT
1 TTAAATGTTGGGGGACTGAAATGCAAGTT
51947 TTAAATGTTGGGGGACCT-AAATGCAAG
1 TTAAATGTTGGGGGA-CTGAAATGCAAG
51974 CTTCTGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.29, C:0.09, G:0.30, T:0.32
Consensus pattern (29 bp):
TTAAATGTTGGGGGACTGAAATGCAAGTT
Found at i:60716 original size:21 final size:19
Alignment explanation
Indices: 60683--60725 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
60673 TTCATGAATT
60683 AAATATTAATTATT-TATTC
1 AAATATTAATTATTAT-TTC
60702 AAATATTTAAATTATTATTTC
1 AAATA-TT-AATTATTATTTC
60723 AAA
1 AAA
60726 CTAAACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 13 0.62
22 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATTAATTATTATTTC
Found at i:62281 original size:3 final size:3
Alignment explanation
Indices: 62273--62301 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
62263 GGTCTATCAA
62273 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
62302 AATCATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:64039 original size:29 final size:28
Alignment explanation
Indices: 63966--64076 Score: 105
Period size: 29 Copynumber: 3.8 Consensus size: 28
63956 TTATTTGTAA
* *
63966 TTATTGTTTAGCCCTTTAACTTTATGTTT
1 TTATTATTTAGTCCTTTAA-TTTATGTTT
* * * *
63995 TTACTATTTTAATCCTTTAAGTTTCTATTT
1 TTATTA-TTTAGTCCTTTAA-TTTATGTTT
*
64025 TTATTATTTAGTCCTGTTAATTTATGTTC
1 TTATTATTTAGTCCT-TTAATTTATGTTT
* *
64054 TTGTTATTTAGTCCTTTATTTTA
1 TTATTATTTAGTCCTTTAATTTA
64077 ATAAGCATGC
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
28 7 0.11
29 32 0.48
30 27 0.41
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (28 bp):
TTATTATTTAGTCCTTTAATTTATGTTT
Found at i:67996 original size:2 final size:2
Alignment explanation
Indices: 67989--68021 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
67979 CCGTAAACAA
67989 AT AT AT AT 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 AT AT AT AT A
68022 CACACACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69960 original size:30 final size:29
Alignment explanation
Indices: 69901--69982 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 29
69891 GGAAAAAATA
* * * *
69901 TTTGTCTCTCTTGAGACAATATATTTGAG
1 TTTGTTTCTCTTGAAACAAAATCTTTGAG
69930 TTTGTTTCTCTTGAAACAAAAGTCTTTGAG
1 TTTGTTTCTCTTGAAACAAAA-TCTTTGAG
* * *
69960 TCTGTTTCTATTAAAACAAAATC
1 TTTGTTTCTCTTGAAACAAAATC
69983 ATCTTTGAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 20 0.44
30 25 0.56
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTGTTTCTCTTGAAACAAAATCTTTGAG
Found at i:69993 original size:32 final size:30
Alignment explanation
Indices: 69924--69998 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
69914 AGACAATATA
* * * *
69924 TTTGAGTTTGTTTCTCTTGAAACAAAAGTC
1 TTTGAGTCTGTTTCTATTAAAACAAAAATC
69954 TTTGAGTCTGTTTCTATTAAAACAAAATCATC
1 TTTGAGTCTGTTTCTATTAAAACAAAA--ATC
69986 TTTGAGTC-GTTTC
1 TTTGAGTCTGTTTC
69999 CCTTGAAACG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 24 0.62
31 5 0.13
32 10 0.26
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (30 bp):
TTTGAGTCTGTTTCTATTAAAACAAAAATC
Found at i:70336 original size:130 final size:128
Alignment explanation
Indices: 70094--70603 Score: 504
Period size: 130 Copynumber: 3.9 Consensus size: 128
70084 GAAAACATGC
* * * *
70094 CGTCCTCATCACGTGGGAACCGTGTTATCATC-CTAAAGATGGCCAGTCGTCCTCATCACATAGG
1 CGTCCTCATCACGTAGGAACCGTGTTATCATCTCTAAAGATGGCTA-ACGTCCTCATCACGTAGG
* * * * * * *
70158 AACCATGTCATCCACCAATCAGACTTCCTCATCACATAGGAGTCGTGTCACCCCTGATAATCGGT
65 AACCGTGTCATCCACCAACCAGACCTCCTCATCACGTAGAAGCCGTGTCACCCCTGATAA-CAGT
* *
70223 CGTCCACATCACGTAGGAACC-TAGTTATCATCTCTAAAGATGGCTTACCGTCCTCATCACGTAG
1 CGTCCTCATCACGTAGGAACCGT-GTTATCATCTCTAAAGATGGC-TAACGTCCTCATCACGTAG
** * * *
70287 GAAATGTGTCATCTACCAACCAAACCTCCTCATCACGTAGAAGCAGTGTCACCCCTAGATAACCA
64 GAACCGTGTCATCCACCAACCAGACCTCCTCATCACGTAGAAGCCGTGTCACCCCT-GATAA-CA
70352 GT
127 GT
* * * * * *
70354 CGTCCTCATCGCGTAGGAACCGTGTTATCGCCCTTTCTAAAGATGGCCAAAC-TCTTTATCACGT
1 CGTCCTCATCACGTAGGAACCGTGTTAT---CATCTCTAAAGATGG-CTAACGTCCTCATCACGT
* *** * * *
70418 ATGAGTTGTGTCATCCACCGACCAGACCTCCTCATCACGTAAAAGCCGTGTCACCCCTAATAACT
62 AGGAACCGTGTCATCCACCAACCAGACCTCCTCATCACGTAGAAGCCGTGTCACCCCTGATAAC-
*
70483 AGC
126 AGT
* * * * * *
70486 CATCCTCATCACGTAGGAATCGTGTTATCATCCCTAAAGATTGTCTGACATCCTCATCACGTAGG
1 CGTCCTCATCACGTAGGAACCGTGTTATCATCTCTAAAGA-TGGCTAACGTCCTCATCACGTAGG
* * * * *
70551 AACCGTGTCATCGACCCACCAGATCTCATCATCACGTAGGAGCCGTGTCACCC
65 AACCGTGTCATCCACCAACCAGACCTCCTCATCACGTAGAAGCCGTGTCACCC
70604 TTAGACGACC
Statistics
Matches: 312, Mismatches: 57, Indels: 23
0.80 0.15 0.06
Matches are distributed among these distances:
128 1 0.00
129 40 0.13
130 129 0.41
131 34 0.11
132 32 0.10
133 60 0.19
134 15 0.05
135 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (128 bp):
CGTCCTCATCACGTAGGAACCGTGTTATCATCTCTAAAGATGGCTAACGTCCTCATCACGTAGGA
ACCGTGTCATCCACCAACCAGACCTCCTCATCACGTAGAAGCCGTGTCACCCCTGATAACAGT
Found at i:70585 original size:263 final size:263
Alignment explanation
Indices: 70163--70641 Score: 606
Period size: 263 Copynumber: 1.8 Consensus size: 263
70153 ATAGGAACCA
* * ** * * * * *
70163 TGTCATCCACCAATCAGACTTCCTCATCACATAGGAGTCGTGTCACCCCTGATAATCGGTCGTCC
1 TGTCATCCACCAACCAGACCTCCTCATCACATAAAAGCCGTGTCACCCCTAATAATCAGCCATCC
* * * *
70228 ACATCACGTAGGAACCTAGTTATCATCTCTAAAGATGGCTTACCGTCCTCATCACGTAGGAAATG
66 ACATCACGTAGGAACCTAGTTATCATCCCTAAAGATGGCTGACCATCCTCATCACGTAGGAAACG
* * * *
70293 TGTCATCTACCAACCAAACCTCCTCATCACGTAGAAGCAGTGTCACCCCTAGATAACCAG-TCGT
131 TGTCATCGACCAACCAAACCTCATCATCACGTAGAAGCAGTGTCACCCCTAGACAACCAGAAC-T
70357 CCTCATCGCGTAGGAACCGTGTTATCGCCCTTTCTAAAGATGGCCAAACTCTTTATCACGTATGA
195 CCTCATCGCGTAGGAACCGTGTTATCGCCCTTTCTAAAGATGGCCAAACTCTTTATCACGTATGA
70422 GTTG
260 GTTG
* *
70426 TGTCATCCACCGACCAGACCTCCTCATCACGTAAAAGCCGTGTCACCCCTAATAA-CTAGCCATC
1 TGTCATCCACCAACCAGACCTCCTCATCACATAAAAGCCGTGTCACCCCTAATAATC-AGCCATC
* * *
70490 CTCATCACGTAGGAATCGT-GTTATCATCCCTAAAGATTGTCTGA-CATCCTCATCACGTAGGAA
65 CACATCACGTAGGAA-CCTAGTTATCATCCCTAAAGA-TGGCTGACCATCCTCATCACGTAGGAA
* * * * * * * *
70553 CCGTGTCATCGACCCACCAGATCTCATCATCACGTAGGAGCCGTGTCACCCTTAGACGACCAGAA
128 ACGTGTCATCGACCAACCAAACCTCATCATCACGTAGAAGCAGTGTCACCCCTAGACAACCAGAA
* *
70618 CTCTTCATCGCGTATGAACCGTGT
193 CTCCTCATCGCGTAGGAACCGTGT
70642 CATCTCTAAT
Statistics
Matches: 180, Mismatches: 32, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
262 1 0.01
263 171 0.95
264 8 0.04
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (263 bp):
TGTCATCCACCAACCAGACCTCCTCATCACATAAAAGCCGTGTCACCCCTAATAATCAGCCATCC
ACATCACGTAGGAACCTAGTTATCATCCCTAAAGATGGCTGACCATCCTCATCACGTAGGAAACG
TGTCATCGACCAACCAAACCTCATCATCACGTAGAAGCAGTGTCACCCCTAGACAACCAGAACTC
CTCATCGCGTAGGAACCGTGTTATCGCCCTTTCTAAAGATGGCCAAACTCTTTATCACGTATGAG
TTG
Found at i:71255 original size:35 final size:35
Alignment explanation
Indices: 71209--71279 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
71199 CCACTAAGCC
*
71209 TCCGCTGATTGCTTCCCCGATGTCTGACGCCGCCA
1 TCCGCTAATTGCTTCCCCGATGTCTGACGCCGCCA
71244 TCCGCTAATTGCTTCCCCGATGTCTGACGCCGCCA
1 TCCGCTAATTGCTTCCCCGATGTCTGACGCCGCCA
71279 T
1 T
71280 TGACAATCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.13, C:0.39, G:0.21, T:0.27
Consensus pattern (35 bp):
TCCGCTAATTGCTTCCCCGATGTCTGACGCCGCCA
Found at i:72595 original size:30 final size:29
Alignment explanation
Indices: 72516--72613 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
72506 GTAATTATTG
* * * *
72516 TTTAGCCCTTTAATTTTCTATTTTTACTAT
1 TTTAGTCC-TTAAATTTCTGTTTTTATTAT
* *
72546 TTTAATCCTTAAGTTTCTGTTTTTATTAT
1 TTTAGTCCTTAAATTTCTGTTTTTATTAT
* * *
72575 TTTAGTCTTGTAAATTTCTGTTCTTGTTA-
1 TTTAGTCCT-TAAATTTCTGTTTTTATTAT
72604 TTTAGTCCTT
1 TTTAGTCCTT
72614 TATTTAATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 1 0.02
29 33 0.59
30 22 0.39
ACGTcount: A:0.18, C:0.13, G:0.08, T:0.60
Consensus pattern (29 bp):
TTTAGTCCTTAAATTTCTGTTTTTATTAT
Done.