Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013943.1 Kokia drynarioides strain JFW-HI SEQ_128973, 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: 154038
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:7933 original size:16 final size:17
Alignment explanation
Indices: 7899--7939 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
7889 ATTTGTCTTC
*
7899 TAATTT-TTAACTTATT
1 TAATTTATTAACTTAGT
7915 TAATTTATTAACTT-GT
1 TAATTTATTAACTTAGT
7931 TAATTTATT
1 TAATTTATT
7940 TTAAATTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (17 bp):
TAATTTATTAACTTAGT
Found at i:7948 original size:18 final size:16
Alignment explanation
Indices: 7914--7952 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
7904 TTTAACTTAT
*
7914 TTAATTTATTAACTTG
1 TTAATTTATTAAATTG
7930 TTAATTTATTTTAAATTG
1 TTAATTTA--TTAAATTG
7948 TTAAT
1 TTAAT
7953 ATTTTTACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
18 12 0.60
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTAATTTATTAAATTG
Found at i:13761 original size:207 final size:209
Alignment explanation
Indices: 13395--13824 Score: 693
Period size: 207 Copynumber: 2.1 Consensus size: 209
13385 TTGCAGTCAA
* * *
13395 TGTCGCGACATAGGTAGTCTTTGTCGCAACATACCTTTTAGATCCTATAGGTCACGACATATTTA
1 TGTCGCAACATAGGTAGTCTTTGTCACAACATACCTTTCAGATCC-ATA-GTCACGACATATTTA
**
13460 GAGGCTTGTCACGACATTCTCCTCAGCCTTGATTTTTTTTTATTTTGGTTCCTTTGTCGCGACAA
64 GAGGCTTGTCACGACATTCTCCTCAGCCTTGATTTTTTTCGATTTTGGTTCCTTTGTCGCGACAA
*
13525 GGAGATATCCATGTCGCGACATTGGCTTCAGTCTTACACTTTCTGGATTCTGTCACCTTTGTTAC
129 GGAGATAGCCATGTCGCGACATTGGCTTCAGTCTTACACTTTCTGGATTCTGTCACCTTTGTTAC
13590 GACACAGCTAATAGTG
194 GACACAGCTAATAGTG
* **
13606 TGTCGCAACATAGGTAGTCTTTGTCATAACATACCTTTCAGATCC-TA-TCACGATGTATTTAGA
1 TGTCGCAACATAGGTAGTCTTTGTCACAACATACCTTTCAGATCCATAGTCACGACATATTTAGA
* *
13669 GGCTTGTCGCGACATTCTCCTCAGCCTTGATTTTTTTCGATTTTGGTTCCTTTGTCGCGATAAGG
66 GGCTTGTCACGACATTCTCCTCAGCCTTGATTTTTTTCGATTTTGGTTCCTTTGTCGCGACAAGG
** **
13734 AGATAGCCATGTCGCGATGTTGGCTTCAGTCTTACACTTTCTGGATTCTGTCACCTTTGTTGTGA
131 AGATAGCCATGTCGCGACATTGGCTTCAGTCTTACACTTTCTGGATTCTGTCACCTTTGTTACGA
13799 CACAGCTAATAGTG
196 CACAGCTAATAGTG
13813 TGTCGCAACATA
1 TGTCGCAACATA
13825 CCCTTATTTT
Statistics
Matches: 204, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
207 161 0.79
209 2 0.01
211 41 0.20
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (209 bp):
TGTCGCAACATAGGTAGTCTTTGTCACAACATACCTTTCAGATCCATAGTCACGACATATTTAGA
GGCTTGTCACGACATTCTCCTCAGCCTTGATTTTTTTCGATTTTGGTTCCTTTGTCGCGACAAGG
AGATAGCCATGTCGCGACATTGGCTTCAGTCTTACACTTTCTGGATTCTGTCACCTTTGTTACGA
CACAGCTAATAGTG
Found at i:14912 original size:35 final size:35
Alignment explanation
Indices: 14866--14939 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
14856 CCTTTACCTG
14866 TTCTTTACCTTCCCTACGAGGATTATTTTCTGTGT
1 TTCTTTACCTTCCCTACGAGGATTATTTTCTGTGT
* *
14901 TTCTTTACCTTCCCTACGGGGATTATTTTTTGTGT
1 TTCTTTACCTTCCCTACGAGGATTATTTTCTGTGT
14936 TTCT
1 TTCT
14940 AGGGATTCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.12, C:0.22, G:0.15, T:0.51
Consensus pattern (35 bp):
TTCTTTACCTTCCCTACGAGGATTATTTTCTGTGT
Found at i:27029 original size:24 final size:22
Alignment explanation
Indices: 27009--27077 Score: 129
Period size: 22 Copynumber: 3.1 Consensus size: 22
26999 CAAACACAAT
27009 CCCGTGTATCCACTCACACACG
1 CCCGTGTATCCACTCACACACG
*
27031 CCCATGTATCCACTCACACACG
1 CCCGTGTATCCACTCACACACG
27053 CCCGTGTATCCACTCACACACG
1 CCCGTGTATCCACTCACACACG
27075 CCC
1 CCC
27078 TTACCCTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.23, C:0.48, G:0.12, T:0.17
Consensus pattern (22 bp):
CCCGTGTATCCACTCACACACG
Found at i:28109 original size:80 final size:80
Alignment explanation
Indices: 28002--28203 Score: 237
Period size: 80 Copynumber: 2.5 Consensus size: 80
27992 AAAACAATGT
* * * ** **
28002 CCGTCAAATCCTAGCACCTAGTGCCTAGCAGATAAATCACAAATGTGTGCTCAACTT-TGGTTGG
1 CCGTCAATTCCTGGCACCTAGTGCCTAGCAGATAAACCACAAATGTAAG-TCAACTTCTAATTGG
28066 ATTAACCAACGAATAA
65 ATTAACCAACGAATAA
* * * * * *
28082 CTGTCAATTCCTGGCACCCAGTGCCTAGC-GAATAAACCGCAATTGTAAGTCTAGTTCTAATTGG
1 CCGTCAATTCCTGGCACCTAGTGCCTAGCAG-ATAAACCACAAATGTAAGTCAACTTCTAATTGG
28146 ATTAACCAACGAATAA
65 ATTAACCAACGAATAA
* *
28162 CCATCAATTCCTGGCACCTAGTGCCTAGCAAATAAACCACAA
1 CCGTCAATTCCTGGCACCTAGTGCCTAGCAGATAAACCACAA
28204 TTGTCAGCCC
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
79 6 0.06
80 95 0.94
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (80 bp):
CCGTCAATTCCTGGCACCTAGTGCCTAGCAGATAAACCACAAATGTAAGTCAACTTCTAATTGGA
TTAACCAACGAATAA
Found at i:29688 original size:24 final size:26
Alignment explanation
Indices: 29630--29699 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 26
29620 CGTTGTAAAA
*
29630 ATTT-CACTTTGATGCTTATCGTTACT
1 ATTTGCACTTTGGTGCTTATCGTTA-T
29656 ATTTTGCACTTTGGTGCTTATCG-T-T
1 A-TTTGCACTTTGGTGCTTATCGTTAT
*
29681 ATTTGCACTTTTGTGCTTA
1 ATTTGCACTTTGGTGCTTA
29700 GTGATATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
24 17 0.43
25 2 0.05
26 1 0.03
27 4 0.10
28 16 0.40
ACGTcount: A:0.16, C:0.17, G:0.16, T:0.51
Consensus pattern (26 bp):
ATTTGCACTTTGGTGCTTATCGTTAT
Found at i:38543 original size:31 final size:31
Alignment explanation
Indices: 38506--38568 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
38496 TAGGTGAAAA
38506 ATGGGTTTAGATGAAGTAATGTGAAAATTAT
1 ATGGGTTTAGATGAAGTAATGTGAAAATTAT
38537 ATGGGTTTAGATGAAGTAATGTGAAAATTAT
1 ATGGGTTTAGATGAAGTAATGTGAAAATTAT
38568 A
1 A
38569 GTGTTGGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (31 bp):
ATGGGTTTAGATGAAGTAATGTGAAAATTAT
Found at i:46487 original size:61 final size:61
Alignment explanation
Indices: 46412--46624 Score: 338
Period size: 61 Copynumber: 3.5 Consensus size: 61
46402 GTAAAAGCAG
* *
46412 AAAGGTCTGATGACTCTGTGTCATCGTGAGTATTAAATGAAATGAATCCTATTACGGATTA
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAAATGAATCCTATTACGGATTA
* *
46473 AAAGGTCTGATGACTTTGTGTCATCGTGAGTATTAAATGAAATGAATCTTATTACGGATTA
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAAATGAATCCTATTACGGATTA
* * *
46534 AAAGGTCCGGTGACTTTGTGTCATCGTGAGTATTAAATGAAATGAATCCTATTATGGACT-
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAAATGAATCCTATTACGGATTA
* *
46594 ATAGGTCCGATGACTTTATGTCATCGTGAGT
1 AAAGGTCCGATGACTTTGTGTCATCGTGAGT
46625 TCAAATGCGA
Statistics
Matches: 142, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
60 28 0.20
61 114 0.80
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.34
Consensus pattern (61 bp):
AAAGGTCCGATGACTTTGTGTCATCGTGAGTATTAAATGAAATGAATCCTATTACGGATTA
Found at i:47374 original size:21 final size:21
Alignment explanation
Indices: 47336--47375 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47326 CAGTGGAAAG
**
47336 GTCACTTGTATCGGTAGAACT
1 GTCACTTGTATCCATAGAACT
47357 GTCACTTGTATCCATAGAA
1 GTCACTTGTATCCATAGAA
47376 GTCAGCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
GTCACTTGTATCCATAGAACT
Found at i:55358 original size:2 final size:2
Alignment explanation
Indices: 55351--55386 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
55341 TATAATTATC
*
55351 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55387 GATAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57116 original size:10 final size:10
Alignment explanation
Indices: 57101--57135 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
57091 TTATGTATTC
57101 TAATTAAATT
1 TAATTAAATT
57111 TAATTAAATAT
1 TAATTAAAT-T
*
57122 TAAATAAATT
1 TAATTAAATT
57132 TAAT
1 TAAT
57136 CTTAAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TAATTAAATT
Found at i:59575 original size:28 final size:28
Alignment explanation
Indices: 59526--59592 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
59516 TTAAATTTTA
59526 TTTTTTATTTTAATTTAACCCTTAGAGTTC
1 TTTTTT-TTTTAATTTAACCCTTAGA-TTC
** *
59556 TTTTTTTTTTAA-TTCGCCCTTATATTC
1 TTTTTTTTTTAATTTAACCCTTAGATTC
59583 TTTTTTTTTT
1 TTTTTTTTTT
59593 CAAATCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.38
28 9 0.26
29 6 0.18
30 6 0.18
ACGTcount: A:0.16, C:0.13, G:0.04, T:0.66
Consensus pattern (28 bp):
TTTTTTTTTTAATTTAACCCTTAGATTC
Found at i:64763 original size:7 final size:7
Alignment explanation
Indices: 64753--64788 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
64743 AAAGAAAAGG
64753 AAGAAGA
1 AAGAAGA
64760 AAGAAGA
1 AAGAAGA
64767 AAGAAGA
1 AAGAAGA
64774 AAGAA-A
1 AAGAAGA
*
64780 AAAAAGA
1 AAGAAGA
64787 AA
1 AA
64789 AAGGAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:64785 original size:23 final size:22
Alignment explanation
Indices: 64759--64805 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
64749 AAGGAAGAAG
64759 AAAGAAGAAA-GAAGAAAGAAAAA
1 AAAGAA-AAAGGAA-AAAGAAAAA
*
64782 AAAGAAAAAGGAAAAAGAGAAA
1 AAAGAAAAAGGAAAAAGAAAAA
64804 AA
1 AA
64806 TGTGAGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAGGAAAAAGAAAAA
Found at i:64787 original size:30 final size:28
Alignment explanation
Indices: 64743--64803 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
64733 AATAAAAAAT
**
64743 AAAGAAAAGGAAGAAGAAA-GAAGAAAGAAG
1 AAAGAAAAAAAAGAA-AAAGGAA-AAAG-AG
64773 AAAGAAAAAAAAGAAAAAGGAAAAAGAG
1 AAAGAAAAAAAAGAAAAAGGAAAAAGAG
64801 AAA
1 AAA
64804 AATGTGAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.18
29 7 0.25
30 16 0.57
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (28 bp):
AAAGAAAAAAAAGAAAAAGGAAAAAGAG
Found at i:64796 original size:15 final size:15
Alignment explanation
Indices: 64728--64805 Score: 59
Period size: 16 Copynumber: 4.9 Consensus size: 15
64718 ATTTCATCCC
*
64728 AAAAAAATA-AAAAAT
1 AAAAAAA-AGAAAAAG
* *
64743 AAAGAAAAGGAAGAAG
1 AAA-AAAAAGAAAAAG
64759 AAAGAAGAAAGAAGAAAG
1 AAA-AA-AAAGAA-AAAG
64777 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
* *
64792 GAAAAAGAGAAAAA
1 AAAAAAAAGAAAAA
64806 TGTGAGGTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
15 19 0.37
16 20 0.38
17 7 0.13
18 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:65784 original size:49 final size:50
Alignment explanation
Indices: 65666--66193 Score: 305
Period size: 49 Copynumber: 10.7 Consensus size: 50
65656 AAACATGGAA
* * * * * * *
65666 ATATAAAGGGAAAGGTTGAGGCCACAATGGCGAACCCAGTACCTTAAAAG
1 ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCTGTACCATAGAAG
* * *
65716 ATGTGATGGG-AAGGATTGAGGCTGCAACGGCGAATCCTGTACCATA-AAG
1 ATATGAAGGGAAAGG-TTGAGGCCGCAACGGCGAATCCTGTACCATAGAAG
*** * * * * *
65765 ATATGAAGGGAAAGGTTGAGATTGTAACGACGAA-CCCGATAACTTAGAAG
1 ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCTG-TACCATAGAAG
* * * * * *
65815 ATGTGATGGGAAAGATTAAGGCCGCAACGACGAATCCAGTACCAT-GAAG
1 ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCTGTACCATAGAAG
* * * * *
65864 ATATGAAGGGAAAGGTTAAGGCCGCAAGGGCGAACCCAGTACCTTAGAAG
1 ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCTGTACCATAGAAG
* * ** * *
65914 ATGTGATGGG-AAGGATTGAGGCTACAACGACGAAT-CTAGTACCATGGAA-
1 ATATGAAGGGAAAGG-TTGAGGCCGCAACGGCGAATCCT-GTACCATAGAAG
* * * * *
65963 ATATAAAGGGAAAGGTTAAGGCCGTAACGGCGAA-GCTAGTACCTTAGAA-
1 ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCT-GTACCATAGAAG
* * ** * ** *
66012 ATGTGATGGGAAAGACTGAGGTCGCAACAACGAAT-CTATTACCATAGAAG
1 ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCT-GTACCATAGAAG
* * *
66062 -TATAAAGGGAAAGGTTGAGGCTGCAACGGCGAA-CCTTGTCCCATAGAAG
1 ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCC-TGTACCATAGAAG
* * * * ** * * *
66111 ATGT-AATAGGAACGATCAAGGCCGCAAAGGCGGAT-CTATTACCATCA-AA-
1 ATATGAA-GGGAAAGGTTGAGGCCGCAACGGCGAATCCT-GTACCAT-AGAAG
*
66160 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAA
1 ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAA
66194 CCTAATACCT
Statistics
Matches: 359, Mismatches: 99, Indels: 41
0.72 0.20 0.08
Matches are distributed among these distances:
48 3 0.01
49 212 0.59
50 140 0.39
51 4 0.01
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (50 bp):
ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAATCCTGTACCATAGAAG
Found at i:65842 original size:99 final size:100
Alignment explanation
Indices: 65666--66195 Score: 549
Period size: 99 Copynumber: 5.4 Consensus size: 100
65656 AAACATGGAA
* * * *
65666 ATATAAAGGGAAAGGTTGAGGCCACAATGGCGAACCC-AGTACCTTAAAAGATGTGATGGGAAGG
1 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGAGTACCTTAGAAGATGTGATGGGAAAG
* *
65730 ATTGAGGCTGCAACGGCGAATCCT-GTACCATAAAG
66 ATTGAGGCCGCAACGACGAAT-CTAGTACCATAAAG
* *** * * *
65765 ATATGAAGGGAAAGGTTGAGATTGTAACGACGAACCCGA-TAACTTAGAAGATGTGATGGGAAAG
1 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGAGTACCTTAGAAGATGTGATGGGAAAG
* * *
65829 ATTAAGGCCGCAACGACGAATCCAGTACCATGAAG
66 ATTGAGGCCGCAACGACGAATCTAGTACCATAAAG
* * * *
65864 ATATGAAGGGAAAGGTTAAGGCCGCAAGGGCGAACCC-AGTACCTTAGAAGATGTGATGGGAAGG
1 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGAGTACCTTAGAAGATGTGATGGGAAAG
** *
65928 ATTGAGGCTACAACGACGAATCTAGTACCATGGAA-
66 ATTGAGGCCGCAACGACGAATCTAGTACCAT-AAAG
* * * *
65963 ATATAAAGGGAAAGGTTAAGGCCGTAACGGCGAA-GCTAGTACCTTAGAA-ATGTGATGGGAAAG
1 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGAGTACCTTAGAAGATGTGATGGGAAAG
* * * *
66026 ACTGAGGTCGCAACAACGAATCTATTACCATAGAAG
66 ATTGAGGCCGCAACGACGAATCTAGTACCATA-AAG
* ** * * * * *
66062 -TATAAAGGGAAAGGTTGAGGCTGCAACGGCGAA-CCTTGTCCCATAGAAGATGTAATAGGAACG
1 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGAGTACCTTAGAAGATGTGATGGGAAAG
** * * * *
66125 ATCAAGGCCGCAAAGGCGGATCTATTACCATCAAA-
66 ATTGAGGCCGCAACGACGAATCTAGTACCAT-AAAG
66160 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
1 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
66196 TAATACCTTA
Statistics
Matches: 360, Mismatches: 60, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
98 84 0.23
99 270 0.75
100 6 0.02
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.18
Consensus pattern (100 bp):
ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGAGTACCTTAGAAGATGTGATGGGAAAG
ATTGAGGCCGCAACGACGAATCTAGTACCATAAAG
Found at i:66235 original size:197 final size:196
Alignment explanation
Indices: 65666--66236 Score: 635
Period size: 197 Copynumber: 2.9 Consensus size: 196
65656 AAACATGGAA
* * *
65666 ATATAAAGGGAAAGGTTGAGGCCACAATGGCGAACCCAGTACCTTAAAAGATGTGATGGGAAGGA
1 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTAGAAGATGTGATGGGAAGGA
* *** *
65731 TTGAGGCTGCAACGGCGAATCCT-GTACCATAAAGATATGAAGGGAAAGGTTGAGATTGTAACGA
66 TTGAGGCTGCAACGGCGAAT-CTAGTACCATAAA-ATATAAAGGGAAAGGTTGAGGCCGTAACGG
** * * * *
65795 CGAACCCGATAACTTA-GAAGATGTGATGGGAAAGATTAAGGCCGCAACGACGAATCCAGTACCA
129 CGAACCTAATACCTTAGGAACA--TGATGGGAAAGATTAAGGTCGCAACAACGAATCCAGTACCA
65859 TGAAG
192 TGAAG
* * *
65864 ATATGAAGGGAAAGGTTAAGGCCGCAAGGGCGAACCCAGTACCTTAGAAGATGTGATGGGAAGGA
1 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTAGAAGATGTGATGGGAAGGA
* * * *
65929 TTGAGGCTACAACGACGAATCTAGTACCATGGAAATATAAAGGGAAAGGTTAAGGCCGTAACGGC
66 TTGAGGCTGCAACGGCGAATCTAGTACCAT-AAAATATAAAGGGAAAGGTTGAGGCCGTAACGGC
* * * ** * * * *
65994 GAAGCTAGTACCTTAGAAATGTGATGGGAAAGACTGAGGTCGCAACAACGAATCTATTACCATAG
130 GAACCTAATACCTTAGGAACATGATGGGAAAGATTAAGGTCGCAACAACGAATCCAGTACCAT-G
66059 AAG
194 AAG
* ** * * * * *
66062 -TATAAAGGGAAAGGTTGAGGCTGCAACGGCGAACCTTGTCCCATAGAAGATGTAATAGGAACGA
1 ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTAGAAGATGTGATGGGAAGGA
** * * * * *
66126 TCAAGGCCGCAAAGGCGGATCTATTACCATCAAAATATAAAGGGAAAGGTTGAGGCCGCAACGGC
66 TTGAGGCTGCAACGGCGAATCTAGTACCAT-AAAATATAAAGGGAAAGGTTGAGGCCGTAACGGC
* *
66191 GAACCTAATACCTTAGGAACATGACGGGAAAGATTAAAGTCGCAAC
130 GAACCTAATACCTTAGGAACATGATGGGAAAGATTAAGGTCGCAAC
66237 GGCGTATCTT
Statistics
Matches: 309, Mismatches: 60, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
197 181 0.59
198 124 0.40
199 4 0.01
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (196 bp):
ATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTAGAAGATGTGATGGGAAGGA
TTGAGGCTGCAACGGCGAATCTAGTACCATAAAATATAAAGGGAAAGGTTGAGGCCGTAACGGCG
AACCTAATACCTTAGGAACATGATGGGAAAGATTAAGGTCGCAACAACGAATCCAGTACCATGAA
G
Found at i:66776 original size:122 final size:122
Alignment explanation
Indices: 66468--66799 Score: 407
Period size: 122 Copynumber: 2.7 Consensus size: 122
66458 GGGTCAGGTT
* * *
66468 AAATCAAGGAAGTGGAGCTCAATTTGAGTGAAACTTCAAACCCCATCTTCCTGATG-GGTTACAG
1 AAATCAATGAAGCGAAGCTCAATTTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGG-TACAG
* * * * * * *
66532 AAAAATGGGTCAGACAATGAAGCGGTCATATTCCTGGTGAGGTACAGAGACGTAGACT
65 AGAAGTGGGTCAAATAATGAAGCGGTCATATTCCTAGTGAGGTACAGAGAAGTAGACC
* * * * * **
66590 AAATCAATGAAGCAAAGCTC-ATTTTAGTAAAACTTCGACACCCCATCTTCTTGATGAGAAACAG
1 AAATCAATGAAGCGAAGCTCAATTTGAGTGAAACTTC-AAACCCCATCTTCCTGATGAGGTACAG
* *
66654 AGAAGTGGGTCAAATAATGAAGCGGTCATTTTCTTAGTGAGGTACAGAGAAGTAGACC
65 AGAAGTGGGTCAAATAATGAAGCGGTCATATTCCTAGTGAGGTACAGAGAAGTAGACC
* * * *
66712 AAATCAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAATCCCATCCTCCTGGTGAGGTACAGA
1 AAATCAATGAAGCGAAGCTCAATTTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGGTACAGA
*
66777 GAAGTAGGTCAAAATAATGAAGC
66 GAAGTGGGTC-AAATAATGAAGC
66800 CGAGCTCAAC
Statistics
Matches: 175, Mismatches: 31, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
121 14 0.08
122 135 0.77
123 26 0.15
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (122 bp):
AAATCAATGAAGCGAAGCTCAATTTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGGTACAGA
GAAGTGGGTCAAATAATGAAGCGGTCATATTCCTAGTGAGGTACAGAGAAGTAGACC
Found at i:69254 original size:2 final size:2
Alignment explanation
Indices: 69239--69272 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
69229 GTTTTCTTCC
69239 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69273 CTTCTAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70773 original size:4 final size:4
Alignment explanation
Indices: 70764--70820 Score: 87
Period size: 4 Copynumber: 14.2 Consensus size: 4
70754 TGGGATTGGA
* *
70764 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAA ACAT ACAT ATAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
70812 ATAT ACAT A
1 ACAT ACAT A
70821 TATTTGTATG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:86188 original size:37 final size:37
Alignment explanation
Indices: 86132--86221 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 37
86122 AGCGGTCACT
*
86132 TTCCTGATGAGATATAGAGAAGTGAACCAAATCCATC
1 TTCCTGATGAGATACAGAGAAGTGAACCAAATCCATC
* * *
86169 TTCCTGATGAAATACAGAGAAGTGAACCAAATTCGTC
1 TTCCTGATGAGATACAGAGAAGTGAACCAAATCCATC
86206 TTCCTGATGAGATACA
1 TTCCTGATGAGATACA
86222 AAGACGTAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (37 bp):
TTCCTGATGAGATACAGAGAAGTGAACCAAATCCATC
Found at i:90692 original size:20 final size:21
Alignment explanation
Indices: 90663--90720 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
90653 ATAAATATTT
*
90663 TATTTTAATATTTAA-AA-AAA
1 TATTTAAATA-TTAATAATAAA
90683 TATTTAAATATTAATAATAAA
1 TATTTAAATATTAATAATAAA
90704 TA-TTATAATATTCAATA
1 TATTTA-AATATT-AATA
90721 TTATTAAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.12
20 14 0.42
21 11 0.33
22 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTAAATATTAATAATAAA
Found at i:90779 original size:16 final size:16
Alignment explanation
Indices: 90758--90807 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
90748 ATATTTAACC
90758 ATATAATAAATTATTA
1 ATATAATAAATTATTA
*
90774 ATATAATATATTATT-
1 ATATAATAAATTATTA
90789 -T-TAATAAATTATTTA
1 ATATAATAAATTA-TTA
90804 ATAT
1 ATAT
90808 TGTAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 9 0.32
14 3 0.11
16 15 0.54
17 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:91469 original size:23 final size:24
Alignment explanation
Indices: 91434--91481 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
91424 AAAAAAAAAG
*
91434 AATTACAAGAGAAAACTAGAAACA
1 AATTACAAGAGAAAACTAAAAACA
*
91458 AATTGCAA-AGAAAACTAAAAACA
1 AATTACAAGAGAAAACTAAAAACA
91481 A
1 A
91482 TTCTGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (24 bp):
AATTACAAGAGAAAACTAAAAACA
Found at i:94081 original size:21 final size:21
Alignment explanation
Indices: 94057--94109 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
94047 ACCCATTTGA
94057 ACCAAACCCAATTGAACCAAG
1 ACCAAACCCAATTGAACCAAG
94078 ACCAAACCCAATTGAACCAAG
1 ACCAAACCCAATTGAACCAAG
*
94099 TCCAAACCCAA
1 ACCAAACCCAA
94110 ACCTAGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.47, C:0.36, G:0.08, T:0.09
Consensus pattern (21 bp):
ACCAAACCCAATTGAACCAAG
Found at i:94096 original size:15 final size:15
Alignment explanation
Indices: 94044--94076 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
94034 GACCCAAAAT
*
94044 CAAACCCATTTGAAC
1 CAAACCCAATTGAAC
94059 CAAACCCAATTGAAC
1 CAAACCCAATTGAAC
94074 CAA
1 CAA
94077 GACCAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.33, G:0.06, T:0.15
Consensus pattern (15 bp):
CAAACCCAATTGAAC
Found at i:94234 original size:65 final size:64
Alignment explanation
Indices: 94129--94258 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 64
94119 AATTGTTGTC
*
94129 CGATTGTTGACCGGCCGTTGACCGTTAACTTTGATCTTTGACTTTTTCGAAAAACCCTACCTTA
1 CGATTGTTGACCGGCCGTTGACCGTTAACTTTGACCTTTGACTTTTTCGAAAAACCCTACCTTA
94193 CNGATTGTTGACCGGCCGTTGACCGTTAACTTTGACCTTTGACTTTTTCGAAAAACCCTACCTTA
1 C-GATTGTTGACCGGCCGTTGACCGTTAACTTTGACCTTTGACTTTTTCGAAAAACCCTACCTTA
94258 C
1 C
94259 CATTTTTCAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 1 0.02
65 63 0.98
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (64 bp):
CGATTGTTGACCGGCCGTTGACCGTTAACTTTGACCTTTGACTTTTTCGAAAAACCCTACCTTA
Found at i:95300 original size:3 final size:3
Alignment explanation
Indices: 95292--95330 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
95282 ATTTACATCA
* *
95292 TAT TAT TAT TAG TAT TAT TAT TAT T-T TGT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
95331 TTGGTTTGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:95325 original size:14 final size:14
Alignment explanation
Indices: 95292--95333 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
95282 ATTTACATCA
* *
95292 TATTATTATTAGTAT
1 TATTATTATT-TTGT
95307 TATTATTATTTTGT
1 TATTATTATTTTGT
95321 TATTATTATTTTG
1 TATTATTATTTTG
95334 GTTTGGGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TATTATTATTTTGT
Found at i:97228 original size:3 final size:3
Alignment explanation
Indices: 97220--97250 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
97210 TTTGACAACC
97220 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
97251 TTGTCCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:98258 original size:21 final size:23
Alignment explanation
Indices: 98214--98259 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
98204 TAAAAATTAC
98214 AAAAATGACCTTTTATATTATTT
1 AAAAATGACCTTTTATATTATTT
* *
98237 AAAAAT-ACTTTTTATCTT-TTT
1 AAAAATGACCTTTTATATTATTT
98258 AA
1 AA
98260 TTTAAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 10 0.48
23 6 0.29
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (23 bp):
AAAAATGACCTTTTATATTATTT
Found at i:100460 original size:7 final size:7
Alignment explanation
Indices: 100430--100465 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
100420 ACTCATCACT
100430 TTAAACC
1 TTAAACC
100437 TTAAATCC
1 TTAAA-CC
100445 TTAATACC
1 TTAA-ACC
100453 TTAAACC
1 TTAAACC
100460 TTAAAC
1 TTAAAC
100466 TAATCACCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 14 0.52
8 12 0.44
9 1 0.04
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (7 bp):
TTAAACC
Found at i:103761 original size:9 final size:9
Alignment explanation
Indices: 103744--103777 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
103734 TTATTATTTA
103744 TAATTTTTT
1 TAATTTTTT
*
103753 TACTTTTTT
1 TAATTTTTT
103762 TAATTTTTT
1 TAATTTTTT
103771 ATAATTT
1 -TAATTT
103778 GAATGGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TAATTTTTT
Found at i:103864 original size:15 final size:15
Alignment explanation
Indices: 103822--103872 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
103812 ATTTATTAAT
*
103822 TTTAATTTTTGTAT-
1 TTTATTTTTTGTATA
* *
103836 TATATTTTGGTGTATA
1 TTTATTTT-TTGTATA
103852 TTTATTTTTTGTATTA
1 TTTATTTTTTGTA-TA
103868 TTTAT
1 TTTAT
103873 GTAAAAAACC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 6 0.21
15 9 0.31
16 14 0.48
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (15 bp):
TTTATTTTTTGTATA
Found at i:105171 original size:114 final size:114
Alignment explanation
Indices: 104888--105188 Score: 315
Period size: 114 Copynumber: 2.7 Consensus size: 114
104878 CTGGATCTTT
* * * * * * *
104888 TGATGAAGAAGAAGACAAGC-GTGCTAATAGAGATAGGAGCGAA-GAAAGTGAGAGAATTCCTG-
1 TGATGAAGAAGATGACAAGCATTCCT-ATAGAGATAGAAG-GAATGAAAGAGAGAAAATTCATGA
*
104950 C--TGATAATGATGGTAAGGATAGGCAGAGAGAAAAACGTCCTAGATCCTC
64 CGGTGATAATGATGGTAAGGATAGGCAGAGAGAAAAACGTCCAAGATCCTC
* ** * *
104999 TGATGAAGAAGATGTCAAGCATTCCTATAGAGATAGAAGGGGTGAACGAGAGAGAATTCATGACG
1 TGATGAAGAAGATGACAAGCATTCCTATAGAGATAGAAGGAATGAAAGAGAGAAAATTCATGACG
* * * * * *
105064 GTGATGATGATGGTAAGGATAGGCGGAGAGAAGAAGGTTCAAGATCTTC
66 GTGATAATGATGGTAAGGATAGGCAGAGAGAAAAACGTCCAAGATCCTC
* * * * * *
105113 TGATGAAGATGATGACAAGCCTTCCTATAGGGATAGAAGGAATGAAAGAGATAAAATTCGTGATG
1 TGATGAAGAAGATGACAAGCATTCCTATAGAGATAGAAGGAATGAAAGAGAGAAAATTCATGACG
*
105178 GTGAAAATGAT
66 GTGATAATGAT
105189 TCCAAGGCTA
Statistics
Matches: 155, Mismatches: 30, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
110 1 0.01
111 46 0.30
112 4 0.03
114 104 0.67
ACGTcount: A:0.39, C:0.10, G:0.31, T:0.21
Consensus pattern (114 bp):
TGATGAAGAAGATGACAAGCATTCCTATAGAGATAGAAGGAATGAAAGAGAGAAAATTCATGACG
GTGATAATGATGGTAAGGATAGGCAGAGAGAAAAACGTCCAAGATCCTC
Found at i:107368 original size:12 final size:12
Alignment explanation
Indices: 107353--107382 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
107343 CAGGTTCAGG
107353 TGATGAGGATGA
1 TGATGAGGATGA
107365 TGATGAGGATGA
1 TGATGAGGATGA
107377 TGATGA
1 TGATGA
107383 ATCTGATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.40, T:0.27
Consensus pattern (12 bp):
TGATGAGGATGA
Found at i:109717 original size:60 final size:59
Alignment explanation
Indices: 109627--110227 Score: 429
Period size: 62 Copynumber: 10.1 Consensus size: 59
109617 TAAAAAACAT
* * * * *
109627 AATTTTTTTGTGTTGCCCATACAATAGCCGACACCCCTATTTATTTGATAAAAAAAATTGC
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCT-TTT-TTTGAGAAAAAAAATTGC
* * * * *
109688 -ATTTTTGGGTGTTGGCCATGCAATGGCCGACATCCCCTTTTCTCGA-ATAAAAAATTAC
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACA-CCCCTTTTTTTGAGAAAAAAAATTGC
* * * * * * *
109746 -ATTTTTGGGTATTGGTCACGCAATGGCTGACA-CCCTCTTTTTGAGAAAAAAAATTTC
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTTGAGAAAAAAAATTGC
* * *
109803 AAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACTTCCTTTTCTCG-GAAAAAAAATTGC
1 --AATTTTTTGGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTTTTGAGAAAAAAAATTGC
* * * *
109864 AAATCTTTTTGGTGTTGGTCATGCAATGGCCGACACCCCCTTTTCTCG-GATAAAAAAATTGTA
1 -AAT-TTTTTGGTGTTGGCCATGCAATGGCCGACA-CCCCTTTTTTTGAGA-AAAAAAATTG-C
* * * *
109927 AATTTTTTTGGTGTTGGCCATGCAATGGCCGACA-CGCTCTTTTTCAGAAAAAAAATTTC
1 AA-TTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTTGAGAAAAAAAATTGC
* ** *
109986 AAAATTTTTTGGTGTTGGCCATGCAATTGTTGACACCTCCTTTTCTTG-GATAAAAAAATTGC
1 --AATTTTTTGGTGTTGGCCATGCAATGGCCGACACC-CCTTTTTTTGAGA-AAAAAAATTGC
** * *
110048 AAATTTTTTTGGTGTTGGCCAT----T--------CCCCTTTTTCAGATAAAAAAATTT-C
1 -AA-TTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTTGAGAAAAAAAATTGC
* *
110096 AAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTTTTCTCG-GATAAAAAAATTGC
1 --AATTTTTTGGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTTTTGAGA-AAAAAAATTGC
* * * *
110158 AAATTTTTTTGGTGTTGGTCATGCAATGGCCGACACCCCTGTTATT-AGATAAAAAAATTTC
1 -AA-TTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTTGAGA-AAAAAAATTGC
110219 ATATTTTTT
1 A-ATTTTTT
110228 TTGTGCATGG
Statistics
Matches: 439, Mismatches: 62, Indels: 79
0.76 0.11 0.14
Matches are distributed among these distances:
48 19 0.04
49 18 0.04
50 3 0.01
52 1 0.00
56 9 0.02
57 10 0.02
58 39 0.09
59 3 0.01
60 113 0.26
61 108 0.25
62 115 0.26
63 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (59 bp):
AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTTGAGAAAAAAAATTGC
Found at i:109855 original size:61 final size:60
Alignment explanation
Indices: 109627--110197 Score: 515
Period size: 60 Copynumber: 9.6 Consensus size: 60
109617 TAAAAAACAT
* * * * * * * *
109627 AATTTTTTTGTGTTGCCCATACAATAGCCGACACCCCTATTTATTTGATAAAAAAAATTGC--
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCT-TTT-CTCG-GAAAAAAAATTTCAA
*
109688 -ATTTTTGGGTGTTGGCCATGCAATGGCCGACATCCCCTTTTCTC-GAATAAAAAA-TT--A
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACA-CCCCTTTTCTCGGAA-AAAAAATTTCAA
* * * * * *
109745 CATTTTTGGGTATTGGTCACGCAATGGCTGACACCCTCTTTT-T-GAGAAAAAAAATTTCAA
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCC-CTTTTCTCG-GAAAAAAAATTTCAA
* *
109805 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACTTCCTTTTCTCGGAAAAAAAATTGC-A
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTCTCGGAAAAAAAATTTCAA
*
109865 AATCTTTTTGGTGTTGGTCATGCAATGGCCGACACCCCCTTTTCTCGGATAAAAAAATTGT-AA
1 AAT-TTTTTGGTGTTGGCCATGCAATGGCCGACA-CCCCTTTTCTCGGA-AAAAAAATT-TCAA
* * *
109928 ATTTTTTTGGTGTTGGCCATGCAATGGCCGACACGCTCTTTT-TCAGAAAAAAAATTTCAA
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTCTCGGAAAAAAAATTTCAA
* ** * *
109988 AATTTTTTGGTGTTGGCCATGCAATTGTTGACACCTCCTTTTCTTGGATAAAAAAATTGCAA
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACC-CCTTTTCTCGGA-AAAAAAATTTCAA
* * * **
110050 ATTTTTTTGGTGTTGGCCAT----T------C-CCCTTTTTC-AGATAAAAAAATTTCAA
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTCTCGGAAAAAAAATTTCAA
*
110098 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTTTTCTCGGATAAAAAAATTGCAA
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTCTCGGA-AAAAAAATTTCAA
* *
110160 ATTTTTTTGGTGTTGGTCATGCAATGGCCGACACCCCT
1 AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCT
110198 GTTATTAGAT
Statistics
Matches: 423, Mismatches: 50, Indels: 74
0.77 0.09 0.14
Matches are distributed among these distances:
48 31 0.07
49 1 0.00
50 6 0.01
51 2 0.00
52 2 0.00
57 13 0.03
58 46 0.11
59 4 0.01
60 121 0.29
61 73 0.17
62 121 0.29
63 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (60 bp):
AATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTTTCTCGGAAAAAAAATTTCAA
Found at i:110101 original size:110 final size:109
Alignment explanation
Indices: 109841--110175 Score: 422
Period size: 110 Copynumber: 2.9 Consensus size: 109
109831 GCCGACACTT
* * * *
109841 CCTTTTCTCGGAAAAAAAATTGC-AAATCTTTTTGGTGTTGGTCATGCAATGGCCGACACCCCCT
1 CCTTTT-TCAGAAAAAAAATTTCAAAAT-TTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCT
*
109905 TTTCTCGGATAAAAAAATTGTAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACAC
64 TTTCTCGGATAAAAAAATTGCAAATTTTTTTGGTGTTGGCCAT----T------C-C
* **
109962 GCTCTTTTTCAGAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATTGTTGACAC-CTCC
1 -C-CTTTTTCAGAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACTC-CC
*
110026 TTTTCTTGGATAAAAAAATTGCAAATTTTTTTGGTGTTGGCCATTCC
63 TTTTCTCGGATAAAAAAATTGCAAATTTTTTTGGTGTTGGCCATTCC
110073 CCTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTT
1 CCTTTTTCAGA-AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTT
110138 TTCTCGGATAAAAAAATTGCAAATTTTTTTGGTGTTGG
65 TTCTCGGATAAAAAAATTGCAAATTTTTTTGGTGTTGG
110176 TCATGCAATG
Statistics
Matches: 196, Mismatches: 12, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
109 10 0.05
110 86 0.44
111 2 0.01
112 1 0.01
118 1 0.01
121 1 0.01
122 86 0.44
123 9 0.05
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (109 bp):
CCTTTTTCAGAAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTTT
TCTCGGATAAAAAAATTGCAAATTTTTTTGGTGTTGGCCATTCC
Found at i:114018 original size:11 final size:12
Alignment explanation
Indices: 113976--114024 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
113966 TATTTGTGTA
113976 AAAATTAATTTG
1 AAAATTAATTTG
113988 AAAATTAATTTTAG
1 AAAATTAA-TTT-G
*
114002 TTGAAATTAATTTG
1 --AAAATTAATTTG
114016 AAAATTAAT
1 AAAATTAAT
114025 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 16 0.52
13 3 0.10
14 2 0.06
15 3 0.10
16 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:114229 original size:86 final size:86
Alignment explanation
Indices: 114125--114773 Score: 858
Period size: 86 Copynumber: 7.6 Consensus size: 86
114115 TACATTTAAA
* * *
114125 ATTAA-TTTAACATTATTTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGT
1 ATTAATTTTAA-A-TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGT
*
114189 GTTAATTTGACAATACATTATTT
64 GTTGATTTGACAATACATTATTT
* * * * * *
114212 ATCAAAATTT-CATATTTAAAGT--ACAA-ATTATTATTAAATTAAAATTTTTATCAAATAATGT
1 AT-TAATTTTAAATATTTAAA-TAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGT
114273 GTTGATTTGACAATACATTATTT
64 GTTGATTTGACAATACATTATTT
* * * * *
114296 ATCAAAATTT-CATATTTAAAGT--ACAA-ATTATTATTAAATTACAA-TTTTATCAAATAATGT
1 AT-TAATTTTAAATATTTAAA-TAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGT
*
114356 GTTGATTTGACAATATATTATTT
64 GTTGATTTGACAATACATTATTT
* *
114379 ATTAATTTTAAATATTTAAATAAAAATTATTA-TATCATATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGT
* *
114443 TGATTTGATAATATATTATTT
66 TGATTTGACAATACATTATTT
* * * * *
114464 ATTAATTTTAAATAATTAAATAAAAATTATTATTATTATATTATAAATTTTATCAAATAATATGT
1 ATTAATTTTAAATATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGT
*
114529 TGATTTGATAATACATTATTT
66 TGATTTGACAATACATTATTT
114550 ATTAATTTTAAATATTTAAAT--AAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGT
*
114612 TGATTTGGCAATACATTATTT
66 TGATTTGACAATACATTATTT
* *
114633 ATTAATTTTAAATATTTAAATAAAAACTATTATTATCATATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGT
*
114698 TGATTTGATAATACATTATTT
66 TGATTTGACAATACATTATTT
* *
114719 ATTAATTTTAAATATTTAAATAAAAATTATTATTATCATATTACAATTTTTATCA
1 ATTAATTTTAAATATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCA
114774 TATTTTAAAT
Statistics
Matches: 514, Mismatches: 36, Indels: 25
0.89 0.06 0.04
Matches are distributed among these distances:
82 6 0.01
83 123 0.24
84 112 0.22
85 79 0.15
86 185 0.36
87 4 0.01
88 2 0.00
89 3 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (86 bp):
ATTAATTTTAAATATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGT
TGATTTGACAATACATTATTT
Found at i:114658 original size:169 final size:170
Alignment explanation
Indices: 114125--114773 Score: 895
Period size: 169 Copynumber: 3.8 Consensus size: 170
114115 TACATTTAAA
** * *
114125 ATTAA-TTTAACATTATTTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGT
1 ATTAATTTTAA-A-TATTTAAATAAAAATTATTATTATTATATTAAAATTT-TATCAAATAATGT
* * * * * *
114189 GTTAATTTGACAATACATTATTTATCAAAATTT-CATATTTAAAGTACAAATTATTAT-T-AAAT
63 GTTGATTTGACAATACATTATTTAT-TAATTTTAAATATTTAAA-TAAAAATTATTATATCATAT
*
114251 TAAAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
126 TACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
* * * * *
114296 ATCAAAATTT-CATATTTAAAGTACAAATTATTATTA--A-ATTACAATTTTATCAAATAATGTG
1 AT-TAATTTTAAATATTTAAA-TAAAAATTATTATTATTATATTAAAATTTTATCAAATAATGTG
*
114357 TTGATTTGACAATATATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATATCATATTAC
64 TTGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATATCATATTAC
* *
114422 AATTTTTATCAAATAATGTGTTGATTTGATAATATATTATTT
129 AATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
* *
114464 ATTAATTTTAAATAATTAAATAAAAATTATTATTATTATATTATAAATTTTATCAAATAATATGT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTA-AAATTTTATCAAATAATGTGT
*
114529 TGATTTGATAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTAT-T-ATATTACA
65 TGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATATCATATTACA
*
114592 ATTTTTATCAAATAATGTGTTGATTTGGCAATACATTATTT
130 ATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
* * *
114633 ATTAATTTTAAATATTTAAATAAAAACTATTATTATCATATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTA-AAATTTTATCAAATAATGTGT
*
114698 TGATTTGATAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATTATCATATTAC
65 TGATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTA-TATCATATTAC
114763 AATTTTTATCA
129 AATTTTTATCA
114774 TATTTTAAAT
Statistics
Matches: 430, Mismatches: 34, Indels: 27
0.88 0.07 0.05
Matches are distributed among these distances:
166 17 0.04
167 64 0.15
168 65 0.15
169 160 0.37
170 14 0.03
171 87 0.20
172 20 0.05
173 3 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (170 bp):
ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTAAAATTTTATCAAATAATGTGTT
GATTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAAATTATTATATCATATTACAA
TTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
Found at i:114980 original size:10 final size:10
Alignment explanation
Indices: 114945--114973 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
114935 CAAATTCGCC
114945 GTTGACCACT
1 GTTGACCACT
114955 GTTGACCACT
1 GTTGACCACT
114965 GTTGACCAC
1 GTTGACCAC
114974 CATTGACTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (10 bp):
GTTGACCACT
Found at i:117248 original size:30 final size:30
Alignment explanation
Indices: 117214--117274 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
117204 GATTTTTTTC
*
117214 CGTTTACT-TTTTAAATTTAATTTGTAATTT
1 CGTTT-CTATTTTAAATTTAATTTCTAATTT
*
117244 CGTTTTTATTTTAAATTTAATTTCTAATTT
1 CGTTTCTATTTTAAATTTAATTTCTAATTT
117274 C
1 C
117275 CTGTATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (30 bp):
CGTTTCTATTTTAAATTTAATTTCTAATTT
Found at i:117284 original size:30 final size:30
Alignment explanation
Indices: 117222--117312 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 30
117212 TCCGTTTACT
* * * *
117222 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
117252 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
* **
117282 TTTT-ATTTTTTTTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTGTATA
117311 TT
1 TT
117313 ATAATTATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 24 0.44
30 30 0.56
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTGTATA
Found at i:118379 original size:62 final size:62
Alignment explanation
Indices: 118185--118381 Score: 292
Period size: 62 Copynumber: 3.2 Consensus size: 62
118175 AAATAAAAAG
* * * * * *
118185 GGGGTGTCAGCCATTGCATGACTAACACCAAAAAAATTTTAAATTTTTTTATTCGA-AA-AA
1 GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCCGAGAACAA
* * *
118245 AGGGTGTCGG-CTTTGCATGGCCAATACCAAAAAAAATTGAAATTTTTTTATCCGAGAACAA
1 GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCCGAGAACAA
118306 GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCCGAGAACAA
1 GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCCGAGAACAA
118368 GGGGTGTCGGCCAT
1 GGGGTGTCGGCCAT
118382 GCCAAAAAAA
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
59 38 0.31
60 10 0.08
61 11 0.09
62 63 0.52
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (62 bp):
GGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCCGAGAACAA
Found at i:119572 original size:165 final size:166
Alignment explanation
Indices: 119371--119691 Score: 626
Period size: 165 Copynumber: 1.9 Consensus size: 166
119361 AAACCTTCGA
119371 ACATCACTACACAGAAAAAAAAAGAGAAAGGAAAGCATATCTCAGAAGCTCATGGTGAATACAAA
1 ACATCACTACACAGAAAAAAAAAGAGAAAGGAAAGCATATCTCAGAAGCTCATGGTGAATACAAA
119436 CCTATGACTCTGGCAAAGGCAGATAAGATACCAACAGAGAATGCTTACGAGCCGTGGATGTTATA
66 CCTATGACTCTGGCAAAGGCAGATAAGATACCAACAGAGAATGCTTACGAGCCGTGGATGTTATA
119501 CCAAAGAAGAAAGTCCAAAACAAGGCATATCTTTGG
131 CCAAAGAAGAAAGTCCAAAACAAGGCATATCTTTGG
119537 ACATCACTACACAG-AAAAAAAAGAGAAAGGAAAGCATATCTCAGAAGCTCATGGTGAATACAAA
1 ACATCACTACACAGAAAAAAAAAGAGAAAGGAAAGCATATCTCAGAAGCTCATGGTGAATACAAA
119601 CCTATGACTCTGGCAAAGGCAGATAAGATACCAACAGAGAATGCTTACGAGCCGTGGATGTTATA
66 CCTATGACTCTGGCAAAGGCAGATAAGATACCAACAGAGAATGCTTACGAGCCGTGGATGTTATA
*
119666 CCAAATAAGAAAGTCCAAAACAAGGC
131 CCAAAGAAGAAAGTCCAAAACAAGGC
119692 TGAACCCAAA
Statistics
Matches: 154, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
165 140 0.91
166 14 0.09
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (166 bp):
ACATCACTACACAGAAAAAAAAAGAGAAAGGAAAGCATATCTCAGAAGCTCATGGTGAATACAAA
CCTATGACTCTGGCAAAGGCAGATAAGATACCAACAGAGAATGCTTACGAGCCGTGGATGTTATA
CCAAAGAAGAAAGTCCAAAACAAGGCATATCTTTGG
Found at i:120702 original size:16 final size:16
Alignment explanation
Indices: 120681--120712 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
120671 TTGAATGCCT
120681 TCTTTAGGTTCTTTCC
1 TCTTTAGGTTCTTTCC
120697 TCTTTAGGTTCTTTCC
1 TCTTTAGGTTCTTTCC
120713 CCCCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.12, T:0.56
Consensus pattern (16 bp):
TCTTTAGGTTCTTTCC
Found at i:121815 original size:21 final size:20
Alignment explanation
Indices: 121765--121815 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
121755 TTTAAAATCC
*
121765 AGTTAAAATGATTTTAAACA
1 AGTTAAAATAATTTTAAACA
*
121785 AGTCAAAATAATTTTCAAACA
1 AGTTAAAATAATTTT-AAACA
*
121806 AGTTATAATA
1 AGTTAAAATA
121816 GCTTTAGGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (20 bp):
AGTTAAAATAATTTTAAACA
Found at i:133720 original size:2 final size:2
Alignment explanation
Indices: 133713--133742 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
133703 ATCCAATTGG
133713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
133743 TTAAATGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:147601 original size:34 final size:34
Alignment explanation
Indices: 147563--147633 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
147553 GTAGCAGCTC
147563 CAACCAAGCACCTTTCGACGCAAACGAACCAAAG
1 CAACCAAGCACCTTTCGACGCAAACGAACCAAAG
147597 CAACCAAGCACCTTTCGACGCAAACGAACCAAAG
1 CAACCAAGCACCTTTCGACGCAAACGAACCAAAG
147631 CAA
1 CAA
147634 ATAAGGAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.42, C:0.35, G:0.14, T:0.08
Consensus pattern (34 bp):
CAACCAAGCACCTTTCGACGCAAACGAACCAAAG
Found at i:152217 original size:21 final size:22
Alignment explanation
Indices: 152191--152242 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
152181 CAAAACCATG
*
152191 AAAACCCAAT-GCCCAAACCCT
1 AAAACCCAATCACCCAAACCCT
*
152212 AAAACCAAATCACCCAAACCCT
1 AAAACCCAATCACCCAAACCCT
152234 -AAACCCAAT
1 AAAACCCAAT
152243 TCGATTTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.48, C:0.40, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAACCCAATCACCCAAACCCT
Done.