Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011953.1 Corchorus olitorius cultivar O-4 contig11986, 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: 52360
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:680 original size:22 final size:22
Alignment explanation
Indices: 655--699 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
645 GCTAGGCCGG
655 CCATGGCCTGGCTACCCGCGCA
1 CCATGGCCTGGCTACCCGCGCA
677 CCATGGCCTGGCTACCCGCGCA
1 CCATGGCCTGGCTACCCGCGCA
699 C
1 C
700 TCTACCCGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (22 bp):
CCATGGCCTGGCTACCCGCGCA
Found at i:3073 original size:18 final size:20
Alignment explanation
Indices: 3042--3079 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
3032 CTCTTCTTCT
3042 TTTTCTCTTCTAGTTCTAGG
1 TTTTCTCTTCTAGTTCTAGG
*
3062 TTTTCT-TT-TAGTTTTAGG
1 TTTTCTCTTCTAGTTCTAGG
3080 GCTAGGGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.11, C:0.13, G:0.16, T:0.61
Consensus pattern (20 bp):
TTTTCTCTTCTAGTTCTAGG
Found at i:4885 original size:13 final size:13
Alignment explanation
Indices: 4867--4892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4857 CTTGGCATGA
4867 GTGATGATTTTTG
1 GTGATGATTTTTG
4880 GTGATGATTTTTG
1 GTGATGATTTTTG
4893 TTGCTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:5271 original size:19 final size:19
Alignment explanation
Indices: 5249--5299 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5239 GGGCTGAAAT
5249 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
5268 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
5287 TAATT-ATTATTAA
1 TAATTAATTATTAA
5300 AAATCCCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:6748 original size:51 final size:50
Alignment explanation
Indices: 6647--6752 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 50
6637 GTTCTTCATA
* **
6647 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
6697 TTTTCTCTTGTTTCA-ATCTTGTCTCTGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
6748 TTTTC
1 TTTTC
6753 ATTCAGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
50 7 0.15
51 40 0.83
52 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:9194 original size:48 final size:48
Alignment explanation
Indices: 9142--9246 Score: 178
Period size: 48 Copynumber: 2.2 Consensus size: 48
9132 TCTTATGTGT
9142 GTTTTTGTGTGCTTGTTCTTGGTGGGAAAAGATG-GCAATTTGTGTATG
1 GTTTTTGTGTGCTTGTTCTTGGTGGGAAAAGATGAG-AATTTGTGTATG
*
9190 GTTTTTGTGTGCTTGTTCTTGGTTGGAAAAGATGAGAATTTGTGTATG
1 GTTTTTGTGTGCTTGTTCTTGGTGGGAAAAGATGAGAATTTGTGTATG
9238 G-TTTTGTGT
1 GTTTTTGTGT
9247 ATGTGTGGAT
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
47 8 0.15
48 46 0.84
49 1 0.02
ACGTcount: A:0.16, C:0.05, G:0.32, T:0.47
Consensus pattern (48 bp):
GTTTTTGTGTGCTTGTTCTTGGTGGGAAAAGATGAGAATTTGTGTATG
Found at i:9822 original size:44 final size:44
Alignment explanation
Indices: 9773--9863 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
9763 TGTGCATTGT
*
9773 TGTATTACTATCTGTTGACTTTGATCTTGT-ATGAGTCAATCTAA
1 TGTATTACTATCTGTTGACTTTGATCTTGTGA-GAGTAAATCTAA
9817 TGTATTACTATCTGTTGACTTTGATCTTGTGAGAGTAAATCTAA
1 TGTATTACTATCTGTTGACTTTGATCTTGTGAGAGTAAATCTAA
9861 TGT
1 TGT
9864 GTGTTGATGT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (44 bp):
TGTATTACTATCTGTTGACTTTGATCTTGTGAGAGTAAATCTAA
Found at i:13230 original size:40 final size:39
Alignment explanation
Indices: 13175--13254 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 39
13165 TTTTTAAGAG
*
13175 AAATATGCTAAACTTGCATAAATTAAATATATCCTTGACA
1 AAATATGCTAAACTTGCATAAATTAAATA-ATCCTTAACA
13215 AAATATGCTAAACTTGCATAAATTAAATAATCCTTAACA
1 AAATATGCTAAACTTGCATAAATTAAATAATCCTTAACA
13254 A
1 A
13255 TAAAGCCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 10 0.26
40 29 0.74
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.31
Consensus pattern (39 bp):
AAATATGCTAAACTTGCATAAATTAAATAATCCTTAACA
Found at i:16202 original size:17 final size:16
Alignment explanation
Indices: 16160--16204 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
16150 ATATCATATT
16160 TTTCCACATATGATTG
1 TTTCCACATATGATTG
*
16176 TTGTCAACATATGATTG
1 TT-TCCACATATGATTG
16193 CTTTCCACATAT
1 -TTTCCACATAT
16205 TATCATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 21 0.84
18 2 0.08
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (16 bp):
TTTCCACATATGATTG
Found at i:17932 original size:2 final size:2
Alignment explanation
Indices: 17919--17952 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
17909 AATATTGGAG
*
17919 AT AT AT AC 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
17953 TCACAATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22650 original size:32 final size:32
Alignment explanation
Indices: 22461--22650 Score: 227
Period size: 32 Copynumber: 5.9 Consensus size: 32
22451 TATTAAAGAA
* *
22461 AACGCCACAGATTAGTGGCGTTTTCCTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
*
22493 AACGCCACAAATTAGTGGCGTTTTCCTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* *
22525 AACGCCACAAATTAGTGGCGTTTTCTTTAATG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* * * *
22557 AACGCCACAAATTAGTGGTGTTTCCTTTAGAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* **
22589 AATGCCACAAATTAGTGGCGTTTAGTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* ** * *
22621 AATGCCACTGATTTGTGGCGTTTTATTCAA
1 AACGCCACAAATTAGTGGCGTTTTCTTCAA
22651 TAAACACCAT
Statistics
Matches: 139, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 139 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (32 bp):
AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
Found at i:23177 original size:33 final size:33
Alignment explanation
Indices: 23135--23257 Score: 153
Period size: 33 Copynumber: 3.7 Consensus size: 33
23125 AACGATCAAT
*
23135 CTCATTTCTTCTATCTTCTTCAATGCGAGCTAG
1 CTCATTTCTTCTATCTTCTTCAATGCGAGCCAG
23168 CTCATTTCTTCTCAT-TTCTTCAACT-CGAGCCAG
1 CTCATTTCTTCT-ATCTTCTTCAA-TGCGAGCCAG
* * *
23201 CTCCTGTCGTCTATCTTCTTCAATGCGAGCCAG
1 CTCATTTCTTCTATCTTCTTCAATGCGAGCCAG
*
23234 CTC-TTGTCTTCTTTCTTCTTCAAT
1 CTCATT-TCTTCTATCTTCTTCAAT
23258 TCTTGCAAGC
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
32 4 0.05
33 71 0.91
34 3 0.04
ACGTcount: A:0.15, C:0.31, G:0.11, T:0.42
Consensus pattern (33 bp):
CTCATTTCTTCTATCTTCTTCAATGCGAGCCAG
Found at i:23269 original size:33 final size:33
Alignment explanation
Indices: 23144--23271 Score: 118
Period size: 33 Copynumber: 3.9 Consensus size: 33
23134 TCTCATTTCT
* *
23144 TCTATCTTCTTCAATGCGAGCTAGCTCATT-TCT
1 TCTATCTTCTTCAATGCGAGCAAGCTC-TTGTCG
* *
23177 TCTCAT-TTCTTCAACT-CGAGCCAGCTCCTGTCG
1 TCT-ATCTTCTTCAA-TGCGAGCAAGCTCTTGTCG
* *
23210 TCTATCTTCTTCAATGCGAGCCAGCTCTTGTCT
1 TCTATCTTCTTCAATGCGAGCAAGCTCTTGTCG
* * **
23243 TCTTTCTTCTTCAATTCTTGCAAGCTCTT
1 TCTATCTTCTTCAATGCGAGCAAGCTCTT
23272 ATTGCCTTTC
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
32 4 0.05
33 73 0.91
34 3 0.04
ACGTcount: A:0.16, C:0.30, G:0.12, T:0.41
Consensus pattern (33 bp):
TCTATCTTCTTCAATGCGAGCAAGCTCTTGTCG
Found at i:28952 original size:27 final size:27
Alignment explanation
Indices: 28894--28952 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
28884 TCGTCCCTTG
28894 CATCACCTACATTCGCATCATCTACAA
1 CATCACCTACATTCGCATCATCTACAA
* *
28921 AATCACCTACATTTGCATCATC-ACCAA
1 CATCACCTACATTCGCATCATCTA-CAA
28948 CATCA
1 CATCA
28953 GATTCATGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.36, C:0.36, G:0.03, T:0.25
Consensus pattern (27 bp):
CATCACCTACATTCGCATCATCTACAA
Found at i:31794 original size:39 final size:39
Alignment explanation
Indices: 31733--32734 Score: 905
Period size: 39 Copynumber: 25.9 Consensus size: 39
31723 AGACGAAATT
** * * *
31733 AAACAACACCTTCCGACGGGGAATGGCAAATTGGAAATAA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAT-A
*
31773 AAACAACACCTTCCGGT-GGGAA-AGCAAACTCGGG-ATA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACT-GGGAATA
* * * * * *
31810 AAACAAAACCTTCCGATAGGGAAGGCCAGACTGGGAAAA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
* *
31849 AAACAACACCTTCCGGTGGGGAAGGGTAAAAC-AGGAATA
1 AAACAACACCTTCCGGTGGGGAAGGG-CAAACTGGGAATA
*
31888 AAAGAAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
1 AAA-CAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
* *
31928 AAAGAACAACTTCCGGTGGGGAAGGGCAAAAC-GGGAATA
1 AAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGGAATA
* * *
31967 AAACAACACCTTCTGGTGGGGAAGGGTAAAAC-AGGAATAA
1 AAACAACACCTTCCGGTGGGGAAGGG-CAAACTGGGAAT-A
* * *
32007 AAACAACACCTTCTGGTGGGGAAAGGCAAACTGGTAATA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
* * * *
32046 AAACAACACCTTCCGGTAGAGAAGGGTAAAAC-AGGAAT-
1 AAACAACACCTTCCGGTGGGGAAGGG-CAAACTGGGAATA
* * *
32084 AAACAACACCTTTCGGTTGGAAAGGGCAAAACT-GGAATA
1 AAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGGAATA
* *
32123 AAACAACACCTTCTGGTGGGGAAGGGCAGACTGGGAATA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
32162 AAACAACACCTTCCGGTGGGGAAGGGCAAAAC-GGGAAT-
1 AAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGGAATA
*
32200 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGTGAATA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
***** * *
32239 AAACAACAAAAAAC-------AA---CAAA--AGAAAGT-
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAA-TA
* *
32266 AAACAACACCTTCCGGCT-GGGATGGGCCAAAC-GTGAATAA
1 AAACAACACCTTCCGG-TGGGGAAGGG-CAAACTGGGAAT-A
32306 AAACAACA-CTTCCCGGTGGGGAAGGGCAAAAC-GGGAATA
1 AAACAACACCTT-CCGGTGGGGAAGGGC-AAACTGGGAATA
* * **
32345 TAAGCAACACCTTCCGGTAGGGAAGGGCGGACTGGGAATA
1 -AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
*
32385 AAACAACACCTTCCGGT-GGGAGAGGGCAATCTGGGAATAA
1 AAACAACACCTTCCGGTGGGGA-AGGGCAAACTGGGAAT-A
* * * *
32425 AAAGAAAACCTTCCGGTAGGGAAGGGCAAAATGGGAATAA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAT-A
*
32465 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
* * *
32504 AAACAACACCTTCCGGTAGGGAAGGGTAAAATGGGAAT-
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
* * * * * *
32542 AAACAACACCTTTCGGTGGGAAAAGTCAAAATGGAAATA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
*** *
32581 AAACAACACCTTTTAGTGGGGAAGGGCAGACTGGGAATA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
* * *
32620 AAACAACACATTCCGGTGGGGAGGGGCAAAAC-GGGAAGA
1 AAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGGAATA
* * * * *
32659 AAACAACACATTCCAGTGGGGAAGAGCAGACTAGGAATA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
* ** *
32698 AAACAACCCCTTCCGGTGGCAAAGGGAAAACTGGGAA
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAA
32735 AAGTGGAAAC
Statistics
Matches: 786, Mismatches: 130, Indels: 93
0.78 0.13 0.09
Matches are distributed among these distances:
27 11 0.01
28 1 0.00
29 4 0.01
32 2 0.00
34 1 0.00
37 20 0.03
38 126 0.16
39 400 0.51
40 214 0.27
41 7 0.01
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.14
Consensus pattern (39 bp):
AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATA
Found at i:31924 original size:79 final size:77
Alignment explanation
Indices: 31733--32734 Score: 817
Period size: 79 Copynumber: 13.0 Consensus size: 77
31723 AGACGAAATT
** * * * *
31733 AAACAACACCTTCCGACGGGGAATGGCAAATTGGAAATAAAAACAACACCTTCCGGT-GGGAAAG
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAA-AAAAACAACACCTTCCGGTGGGGAAGG
* *
31797 CAAACTCGGG-ATA
65 GAAA-ACGGGAATA
* * * * *
31810 AAACAAAACCTTCCGATAGGGAAGGCCAGACTGGGAAAAAAACAACACCTTCCGGTGGGGAAGGG
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGGGGAAGGG
*
31875 TAAAACAGGAATA
66 -AAAACGGGAATA
* * * *
31888 AAAGAAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATAAAAGAACAACTTCCGGTGGGGAAGG
1 AAA-CAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGGGGAAGG
31953 GCAAAACGGGAATA
65 G-AAAACGGGAATA
* * * * *
31967 AAACAACACCTTCTGGTGGGGAAGGGTAAAAC-AGGAATAAAAACAACACCTTCTGGTGGGGAAA
1 AAACAACACCTTCCGGTGGGGAAGGG-CAAACTGGGAA-AAAAACAACACCTTCCGGTGGGGAAG
* *
32031 GGCAAACTGGTAATA
64 GGAAAAC-GGGAATA
* * * * * * * *
32046 AAACAACACCTTCCGGTAGAGAAGGGTAAAAC-AGG-AATAAACAACACCTTTCGGTTGGAAAGG
1 AAACAACACCTTCCGGTGGGGAAGGG-CAAACTGGGAAAAAAACAACACCTTCCGGTGGGGAAGG
*
32109 GCAAAACTGGAATA
65 G-AAAACGGGAATA
* * *
32123 AAACAACACCTTCTGGTGGGGAAGGGCAGACTGGGAATAAAACAACACCTTCCGGTGGGGAAGGG
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGGGGAAGGG
32188 CAAAACGGGAAT-
66 -AAAACGGGAATA
* * ***** *
32200 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGTGAATAAAACAACAAAAAAC-------AA--C
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGGGGAAGGG
*
32256 AAAA--GAAAGT-
66 AAAACGGGAA-TA
* *
32266 AAACAACACCTTCCGGCT-GGGATGGGCCAAAC-GTGAATAAAAACAACA-CTTCCCGGTGGGGA
1 AAACAACACCTTCCGG-TGGGGAAGGG-CAAACTGGGAA-AAAAACAACACCTT-CCGGTGGGGA
32328 AGGGCAAAACGGGAATA
62 AGGG-AAAACGGGAATA
* * ** *
32345 TAAGCAACACCTTCCGGTAGGGAAGGGCGGACTGGGAATAAAACAACACCTTCCGGT-GGGAGAG
1 -AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGGGGA-AG
* *
32409 GGCAATCTGGGAATAA
64 GGAAAAC-GGGAAT-A
* * * *
32425 AAAGAAAACCTTCCGGTAGGGAAGGGCAAAATGGGAATAAAAACAACACCTTCCGGTGGGGAAGG
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAA-AAAAACAACACCTTCCGGTGGGGAAGG
* *
32490 GCAAACTGGTAATA
65 GAAAAC-GGGAATA
* * * * * * *
32504 AAACAACACCTTCCGGTAGGGAAGGGTAAAATGGG-AATAAACAACACCTTTCGGTGGGAAAAGT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGGG-GAAGG
* * *
32568 CAAAATGGAAATA
65 GAAAACGGGAATA
*** * * * *
32581 AAACAACACCTTTTAGTGGGGAAGGGCAGACTGGGAATAAAACAACACATTCCGGTGGGGAGGGG
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGGGGAAGGG
*
32646 CAAAACGGGAAGA
66 -AAAACGGGAATA
* * * * * * * **
32659 AAACAACACATTCCAGTGGGGAAGAGCAGACTAGGAATAAAACAACCCCTTCCGGTGGCAAAGGG
1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGGGGAAGGG
32724 AAAACTGGGAA
66 AAAAC-GGGAA
32735 AAGTGGAAAC
Statistics
Matches: 752, Mismatches: 132, Indels: 81
0.78 0.14 0.08
Matches are distributed among these distances:
65 3 0.00
66 29 0.04
67 20 0.03
70 2 0.00
74 2 0.00
76 22 0.03
77 200 0.27
78 181 0.24
79 227 0.30
80 62 0.08
81 4 0.01
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.14
Consensus pattern (77 bp):
AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAAAAACAACACCTTCCGGTGGGGAAGGG
AAAACGGGAATA
Found at i:32477 original size:119 final size:118
Alignment explanation
Indices: 32266--32734 Score: 465
Period size: 119 Copynumber: 4.0 Consensus size: 118
32256 AAAAGAAAGT
* *
32266 AAACAACACCTTCCGGCTGGGATG-GGCCAAAC-GTGAATAAAAACAACA-CTTCCCGGTGGGGA
1 AAACAACACCTTCCGG-TGGGA-GAGGGCAAACTGGGAATAAAAACAACACCTT-CCGGT-GGGA
* * * * *
32328 AGGGCAAAACGGGAATATAAGCAACACCTTCCGGTAGGGAAGGGCGGACTGGGAATA
62 AGGGCAAAATGGGAATAAAAACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAATA
* * *
32385 AAACAACACCTTCCGGTGGGAGAGGGCAATCTGGGAATAAAAAGAAAACCTTCCGGTAGGGAAGG
1 AAACAACACCTTCCGGTGGGAGAGGGCAAACTGGGAATAAAAACAACACCTTCCGGT-GGGAAGG
* *
32450 GCAAAATGGGAATAAAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATA
65 GCAAAATGGGAATAAAAACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAATA
* * * *
32504 AAACAACACCTTCCGGTAGGGA-AGGGTAAAATGGGAAT--AAACAACACCTTTCGGTGGGAAAA
1 AAACAACACCTTCCGGT-GGGAGAGGGCAAACTGGGAATAAAAACAACACCTTCCGGTGGG-AAG
* * ***
32566 GTCAAAATGGAAAT-AAAACAACACCTTTTAGTGGGGAAGGGCAGACTGGGAATA
64 GGCAAAATGGGAATAAAAACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAATA
* * * *
32620 AAACAACACATTCCGGTGGG-GAGGGGCAAAAC-GGGAA-GAAAACAACACATTCCAGTGGGGAA
1 AAACAACACCTTCCGGTGGGAGA-GGGC-AAACTGGGAATAAAAACAACACCTTCCGGT-GGGAA
* * * * * ** * *
32682 GAGCAGACTAGGAAT-AAAACAACCCCTTCCGGTGGCAAAGGGAAAACTGGGAA
63 GGGCAAAATGGGAATAAAAACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAA
32735 AAGTGGAAAC
Statistics
Matches: 291, Mismatches: 48, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
115 4 0.01
116 62 0.21
117 86 0.30
118 14 0.05
119 118 0.41
120 7 0.02
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (118 bp):
AAACAACACCTTCCGGTGGGAGAGGGCAAACTGGGAATAAAAACAACACCTTCCGGTGGGAAGGG
CAAAATGGGAATAAAAACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAATA
Found at i:34506 original size:50 final size:49
Alignment explanation
Indices: 34427--34584 Score: 255
Period size: 50 Copynumber: 3.2 Consensus size: 49
34417 TGTTTTCTAG
34427 CTTAAAGATTTCA-TTTTATTACAAATTAATCAAAAATTCAAACTTTTTA
1 CTTAAAGATTTCATTTTTATTACAAATTAATCAAAAATT-AAACTTTTTA
34476 CTTAAAGATTTCATTTTTATTACAAATTAATCAAAAATTTAAACTTTTTA
1 CTTAAAGATTTCATTTTTATTACAAATTAATCAAAAA-TTAAACTTTTTA
* * *
34526 CTTAAAGATTTCATCTTTATTACAAATTAATCAAAAATTTAACATTTTA
1 CTTAAAGATTTCATTTTTATTACAAATTAATCAAAAATTAAACTTTTTA
34575 GCTTAAAGAT
1 -CTTAAAGAT
34585 CACAAATTAA
Statistics
Matches: 103, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
49 23 0.22
50 78 0.76
51 2 0.02
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.43
Consensus pattern (49 bp):
CTTAAAGATTTCATTTTTATTACAAATTAATCAAAAATTAAACTTTTTA
Found at i:34590 original size:39 final size:40
Alignment explanation
Indices: 34547--34623 Score: 122
Period size: 39 Copynumber: 1.9 Consensus size: 40
34537 CATCTTTATT
*
34547 ACAAATTAATCAAAAATTTAA-CATTTTAGCTT-AAAGATC
1 ACAAATTAATCAAAAATTCAATC-TTTTAGCTTCAAAGATC
34586 ACAAATTAATCAAAAATTCAATCTTTTAGCTTCAAAGA
1 ACAAATTAATCAAAAATTCAATCTTTTAGCTTCAAAGA
34624 CTTCATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 29 0.83
40 6 0.17
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.32
Consensus pattern (40 bp):
ACAAATTAATCAAAAATTCAATCTTTTAGCTTCAAAGATC
Found at i:34603 original size:100 final size:100
Alignment explanation
Indices: 34427--34608 Score: 251
Period size: 100 Copynumber: 1.8 Consensus size: 100
34417 TGTTTTCTAG
* ** **
34427 CTTAAAGATTTCATTTTATTACAAATTAATCAAAAATTCAAACTTTTTACTTAAAGATTTCATTT
1 CTTAAAGATTTCATTTTATTACAAATTAATCAAAAATTCAAACATTTTACTTAAAGATCACAAAT
* * *
34492 TTATTACAAATT-AATCAAAAATTTAAACTTTTTA
66 TAATCAAAAATTCAATCAAAAATTTAAACTTTTTA
*
34526 CTTAAAGATTTCATCTTTATTACAAATTAATCAAAAATT-TAACATTTTAGCTTAAAGATCACAA
1 CTTAAAGATTTCAT-TTTATTACAAATTAATCAAAAATTCAAACATTTTA-CTTAAAGATCACAA
34590 ATTAATCAAAAATTCAATC
64 ATTAATCAAAAATTCAATC
34609 TTTTAGCTTC
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
99 22 0.31
100 45 0.63
101 4 0.06
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.41
Consensus pattern (100 bp):
CTTAAAGATTTCATTTTATTACAAATTAATCAAAAATTCAAACATTTTACTTAAAGATCACAAAT
TAATCAAAAATTCAATCAAAAATTTAAACTTTTTA
Found at i:34670 original size:89 final size:88
Alignment explanation
Indices: 34497--34670 Score: 208
Period size: 89 Copynumber: 2.0 Consensus size: 88
34487 CATTTTTATT
* * * *
34497 ACAAATTAATCAAAAATTTAAACTTTTTACTTAAAGATTTCATCTTTATTACAAATTAATCAAAA
1 ACAAATTAATCAAAAATTCAAACTTTTTACTTAAAGACTTCATCTTTAGTACAAACTAATCAAAA
* * *
34562 ATTTAACATTTTAGCTTAAAGATC
66 ATTCAACA-TTAAGATTAAAGATC
* * *
34586 ACAAATTAATCAAAAATTCAATC-TTTTAGCTTCAAAGACTTCATTTTTAGTATAAACTAATCAA
1 ACAAATTAATCAAAAATTCAAACTTTTTA-CTT-AAAGACTTCATCTTTAGTACAAACTAATCAA
34650 AAATTCAATC-TTAAGATTAAA
64 AAATTCAA-CATTAAGATTAAA
34671 CTTTTCATCA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
88 5 0.07
89 33 0.46
90 33 0.46
91 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.37
Consensus pattern (88 bp):
ACAAATTAATCAAAAATTCAAACTTTTTACTTAAAGACTTCATCTTTAGTACAAACTAATCAAAA
ATTCAACATTAAGATTAAAGATC
Found at i:39394 original size:10 final size:10
Alignment explanation
Indices: 39368--39459 Score: 51
Period size: 10 Copynumber: 10.1 Consensus size: 10
39358 CAAGATTCCA
39368 ATTATT-ATT
1 ATTATTAATT
39377 -TT-TTAATT
1 ATTATTAATT
39385 ATTATTAATT
1 ATTATTAATT
39395 A-T-TT-A--
1 ATTATTAATT
39400 ATTATTAATT
1 ATTATTAATT
39410 ATTATTAATT
1 ATTATTAATT
* *
39420 -TAAATT-GTT
1 AT-TATTAATT
39429 ATTATTAATT
1 ATTATTAATT
* * *
39439 CTAATTAATA
1 ATTATTAATT
*
39449 ATTAATAATT
1 ATTATTAATT
39459 A
1 A
39460 AAAACAAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 21
0.66 0.12 0.23
Matches are distributed among these distances:
5 1 0.02
6 1 0.02
7 5 0.08
8 8 0.13
9 9 0.15
10 37 0.61
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (10 bp):
ATTATTAATT
Found at i:39397 original size:7 final size:7
Alignment explanation
Indices: 39385--39459 Score: 57
Period size: 7 Copynumber: 10.6 Consensus size: 7
39375 TTTTTTAATT
39385 ATTATTA
1 ATTATTA
39392 ATTATTTA
1 ATTA-TTA
39400 ATTATTA
1 ATTATTA
39407 ATTATT-
1 ATTATTA
39413 ATTAATTTAA
1 ATT-A-TT-A
*
39423 ATTGTT-
1 ATTATTA
39429 ATTATTA
1 ATTATTA
*
39436 ATT-CTA
1 ATTATTA
*
39442 ATTAATA
1 ATTATTA
*
39449 ATTAATA
1 ATTATTA
39456 ATTA
1 ATTA
39460 AAAACAAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
6 13 0.23
7 30 0.53
8 11 0.19
10 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (7 bp):
ATTATTA
Found at i:39435 original size:25 final size:24
Alignment explanation
Indices: 39382--39435 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
39372 TTATTTTTTA
39382 ATTATTATTAATTATTTAATTATT
1 ATTATTATTAATTATTTAATTATT
* *
39406 AATTATTATTAA-T-TTAAATTGTT
1 -ATTATTATTAATTATTTAATTATT
39429 ATTATTA
1 ATTATTA
39436 ATTCTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 7 0.26
23 8 0.30
24 1 0.04
25 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTATTATTAATTATTTAATTATT
Found at i:39802 original size:15 final size:15
Alignment explanation
Indices: 39782--39824 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
39772 AAGGAAATAT
39782 TTTTTGATTTTTGAA
1 TTTTTGATTTTTGAA
*
39797 TTTTTGA--TTTGAT
1 TTTTTGATTTTTGAA
*
39810 TTTTTTATTTTTGAA
1 TTTTTGATTTTTGAA
39825 AACCTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 11 0.48
15 12 0.52
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.70
Consensus pattern (15 bp):
TTTTTGATTTTTGAA
Found at i:39809 original size:20 final size:20
Alignment explanation
Indices: 39784--39823 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39774 GGAAATATTT
39784 TTTGATTTTTGAATTTTTGA
1 TTTGATTTTTGAATTTTTGA
**
39804 TTTGATTTTTTTATTTTTGA
1 TTTGATTTTTGAATTTTTGA
39824 AAACCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.70
Consensus pattern (20 bp):
TTTGATTTTTGAATTTTTGA
Found at i:45755 original size:68 final size:68
Alignment explanation
Indices: 45398--46087 Score: 629
Period size: 68 Copynumber: 10.5 Consensus size: 68
45388 AGTAAAGTTC
* *
45398 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTTA-TTTTGTCTTCTCGCATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTCTTGCATTTAAGTT
* *
45462 CAA
66 TAG
* * *
45465 TACTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTT-TTGCATTTAAGTC
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTCTTGCATTTAAGTT
45529 TAG
66 TAG
* * * *
45532 TATTTTCTATTTCCAAAAATACCCTTTCGGTCG-AGGGTCATTTTCGGCTTCTTGCATATAAG-C
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTCTTGCATTTAAGTT
*
45595 T-C
66 TAG
** * *
45597 TATTTTCTATTTCCGGAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCCTT-TTGCATTTGAGT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGT-CTTCTTGCATTTAAGT
45661 TTA-
65 TTAG
* * * *
45664 -CTTTT-GATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTTTCTTCTCGCATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTCTTGCATTTAAGTT
45727 TAG
66 TAG
* * * *
45730 TATTTTCTATTTCCAAAAATACCCTTTTGGTCGGAGGGTCGTTTTTGTCTTCTTGCATTTAAGTC
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTCTTGCATTTAAGTT
45795 TAG
66 TAG
* * * * * *
45798 TATTTTTTATTTTCAATAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTG--TGT---TT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTCTTGCATTTAAGTT
45858 TAG
66 TAG
** * * * * * **
45861 --TTTAGTATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCGTTTTCGTCTTTTTGTACCTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTCTTGCATTTAAGTT
45924 TAG
66 TAG
* * * * * * *** * *
45927 TACTTTCTTTTTCAAAAAATGCCCTTTCGGTCGAAGGGCCAATTTCAACTT-TTCCATATCCAAG
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTCTTGCAT-T-TAAG
45991 -TTAG
64 TTTAG
* * * * * * *
45995 --TTTACT-TTTCCCAAAATACCCTTTCGATCAAAGGGTCAATTTTGTCCTTTTTGCATTTGAGT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGT-CTTCTTGCATTTAAGT
46057 TTA-
65 TTAG
* * *
46060 -CTTTT-GATTACC-AAAATACCCTTTCGGT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGT
46088 GAAAAGGTCA
Statistics
Matches: 513, Mismatches: 86, Indels: 50
0.79 0.13 0.08
Matches are distributed among these distances:
61 47 0.09
63 5 0.01
64 3 0.01
65 127 0.25
66 68 0.13
67 107 0.21
68 153 0.30
69 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (68 bp):
TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTCTTGCATTTAAGTT
TAG
Found at i:45873 original size:197 final size:196
Alignment explanation
Indices: 45396--46087 Score: 706
Period size: 197 Copynumber: 3.5 Consensus size: 196
45386 AAAGTAAAGT
* * * *
45396 TCTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTTATTTT-GT-CTTCTCGCATTTAA
1 TCTATTTTCTATTTCCGAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCCTT-TTGCATTTGA
* **
45459 GTTCAATACTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTTTGCATTT
65 GTT---TA-TGT-GATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTTTGCATTT
*
45524 AAGTCTAGTATTTTCTATTTCCAAAAATACCCTTTCGGTC-GAGGGTCATTTTCGGCTTCTTGCA
125 AAGTTTAGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGGAGGGTCATTTTCGGCTTCTTGCA
45588 TATAAGC
190 TATAAGC
*
45595 TCTATTTTCTATTTCCGGAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCCTTTTGCATTTGAG
1 TCTATTTTCTATTTCCGAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCCTTTTGCATTTGAG
* * *
45660 TTTACTTTTGATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTTTCTTCTCGCATTTAAG
66 TTTA--TGTGATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTT-TTGCATTTAAG
* * * * *
45725 TTTAGTATTTTCTATTTCCAAAAATACCCTTTTGGTCGGAGGGTCGTTTTTGTCTTCTTGCATTT
128 TTTAGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGGAGGGTCATTTTCGGCTTCTTGCATAT
45790 AAGTC
193 AAG-C
* * * * ** *
45795 TAGTATTTTTTATTTTC-AATAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTGTTTT
1 T-CTATTTTCTATTTCCGAA-AATACCCTTTCGGTCGAAGGGTCATTTTCGTCCTTTTGCATTTG
* * * * **
45859 AGTTTA-GT-ATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCGTTTTCGTCTTTTTGTACCTAAG
64 AGTTTATGTGATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTC-TTTTGCATTTAAG
* * * * * * * ** *
45922 TTTAGTACTTTCTTTTTCAAAAAATGCCCTTTCGGTCGAAGGGCCAATTTCAACTT-TTCCATAT
128 TTTAGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGGAGGGTCATTTTCGGCTTCTTGCATAT
45986 CCAAG-
193 --AAGC
* * * *
45991 T-TAGTTTACT-TTTCCCAAAATACCCTTTCGATCAAAGGGTCAATTTT-GTCCTTTTTGCATTT
1 TCTA-TTTTCTATTTCCGAAAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTCC-TTTTGCATTT
* *
46053 GAGTTTACTTTTGATTACC-AAAATACCCTTTCGGT
63 GAGTTTA--TGTGATTTCCAAAAATACCCTTTCGGT
46088 GAAAAGGTCA
Statistics
Matches: 415, Mismatches: 59, Indels: 39
0.81 0.12 0.08
Matches are distributed among these distances:
194 30 0.07
195 25 0.06
196 7 0.02
197 131 0.32
198 70 0.17
199 75 0.18
200 16 0.04
201 61 0.15
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44
Consensus pattern (196 bp):
TCTATTTTCTATTTCCGAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCCTTTTGCATTTGAG
TTTATGTGATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTTTGCATTTAAGTTT
AGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGGAGGGTCATTTTCGGCTTCTTGCATATAAG
C
Found at i:45889 original size:61 final size:61
Alignment explanation
Indices: 45805--45964 Score: 185
Period size: 61 Copynumber: 2.5 Consensus size: 61
45795 TAGTATTTTT
* * * *** *
45805 TATTTTCAATAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTGTTTTAGTTTAG
1 TATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTACCTAAGTTTAG
*
45866 TATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCGTTTTCGTCTTTTTGTACCTAAGTTTAG
1 TATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTACCTAAGTTTAG
45927 TACTTTCTTTTTCAAAAAATGCCCTTTCGGTCGAAGGG
1 TA-TTTC-----C-AAAAATGCCCTTTCGGTCGAAGGG
45965 CCAATTTCAA
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
61 55 0.65
62 4 0.05
67 1 0.01
68 24 0.29
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (61 bp):
TATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTACCTAAGTTTAG
Found at i:45995 original size:129 final size:130
Alignment explanation
Indices: 45474--46031 Score: 366
Period size: 129 Copynumber: 4.2 Consensus size: 130
45464 ATACTTTCTT
* * ** *
45474 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTT-TTGCATTTAAGTCTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTCGTCTTCTTGCACCTAAGTCTAGTACTTT
* * * **
45538 CTATTTCCAAAAATACCCTTTCGGTCG-AGGGTCATTTTCGGCTTCTTGCATAT--AAGCTCTAT
66 CTATTTTCAAAAATACCCTTTCGGTCGAAGGGCCAATTTCAACTT-TT-CATATCCAAG-T-T-T
**
45600 TTTCTA
126 AGT-TA
** * ** *
45606 TTTCCGGAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCCTT-TTGCATTTGAGT-T--TACTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTCGT-CTTCTTGCACCTAAGTCTAGTACTT
* * * *** * ** **
45667 T-TGATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTTTCTTCTCGCATTTAAGTTTAGT
65 TCT-ATTTTCAAAAATACCCTTTCGGTCGAAGGGCCAATTTCAACTTTTCATATCCAAGTTTAG-
45731 ATTTTCTA
128 ----T-TA
* * * ** *
45739 TTTCCAAAAATACCCTTTTGGTCGGAGGGTCGTTTTTGTCTTCTTGCATTTAAGTCTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTCGTCTTCTTGCACCTAAGTCTAGTACTTT
* * * * ** ** * ***
45804 TTATTTTCAATAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTGTTTTAGTTTAG-TA
66 CTATTTTCAAAAATACCCTTTCGGTCGAAGGGCCAATTTCAACTTTTCATATCCAAGTTTAGTTA
* * * *
45868 TTTCCAAAAATGCCCTTTCGGTCGAAGGGTCGTTTTCGTCTTTTTGTACCTAAGTTTAGTACTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTCGTCTTCTTGCACCTAAGTCTAGTACTTT
*
45933 CT-TTTTCAAAAAATGCCCTTTCGGTCGAAGGGCCAATTTCAACTTTTCCATATCCAAG-TTAGT
66 CTATTTTC-AAAAATACCCTTTCGGTCGAAGGGCCAATTTCAACTTTT-CATATCCAAGTTTAG-
45996 TTA
128 TTA
* * *
45999 CTTTTCCCAAAATACCCTTTCGATCAAAGGGTC
1 --TTTCCAAAAATACCCTTTCGGTCGAAGGGTC
46032 AATTTTGTCC
Statistics
Matches: 348, Mismatches: 57, Indels: 41
0.78 0.13 0.09
Matches are distributed among these distances:
128 6 0.02
129 100 0.29
130 36 0.10
131 19 0.05
132 40 0.11
133 89 0.26
134 1 0.00
136 56 0.16
137 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (130 bp):
TTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTCGTCTTCTTGCACCTAAGTCTAGTACTTT
CTATTTTCAAAAATACCCTTTCGGTCGAAGGGCCAATTTCAACTTTTCATATCCAAGTTTAGTTA
Found at i:46116 original size:65 final size:64
Alignment explanation
Indices: 46005--46156 Score: 153
Period size: 65 Copynumber: 2.3 Consensus size: 64
45995 TTTACTTTTC
* * * ** * ** *
46005 CCAAAATACCCTTTCGATCAAAGGGTCAATTTTGTCCTTTTTGCATTTGAGTTTACTTTTGA-TT
1 CCAAAATACCCTTTCGGTGAAAAGGTCAATTTCATCATTTCCGCATTTGAGTTTA-TTCT-ACTT
46069 A
64 A
* * *
46070 CCAAAATACCCTTTCGGTGAAAAGGTCAGTTTCATCATTTCCGCATTTTAGTTTATTCTACTTTC
1 CCAAAATACCCTTTCGGTGAAAAGGTCAATTTCATCATTTCCGCATTTGAGTTTATTCTAC-TTA
*
46135 CCAAAATGCCCTTTCGGTGAAA
1 CCAAAATACCCTTTCGGTGAAA
46157 GGGCAAGCTT
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 1 0.01
64 3 0.04
65 68 0.94
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (64 bp):
CCAAAATACCCTTTCGGTGAAAAGGTCAATTTCATCATTTCCGCATTTGAGTTTATTCTACTTA
Found at i:47754 original size:8 final size:8
Alignment explanation
Indices: 47738--48447 Score: 309
Period size: 8 Copynumber: 95.2 Consensus size: 8
47728 AATTGAAATA
47738 AAGAATTG
1 AAGAATTG
*
47746 AATAATTG
1 AAGAATTG
*
47754 AATAATTG
1 AAGAATTG
47762 AA-ACATTG
1 AAGA-ATTG
*
47770 AATAATTG
1 AAGAATTG
*
47778 AAGAGTTG
1 AAGAATTG
47786 AAGAATTG
1 AAGAATTG
*
47794 AATAATTG
1 AAGAATTG
*
47802 GAGAATTG
1 AAGAATTG
*
47810 AAGCATTG
1 AAGAATTG
**
47818 AAGCGTTG
1 AAGAATTG
*
47826 AATAATTG
1 AAGAATTG
*
47834 AAGAACTG
1 AAGAATTG
*
47842 AATG-ACTG
1 AA-GAATTG
*
47850 AGGAATTG
1 AAGAATTG
*
47858 AAGCATTG
1 AAGAATTG
*
47866 AATAATTG
1 AAGAATTG
*
47874 -A-ACTTG
1 AAGAATTG
*
47880 AAGCATTG
1 AAGAATTG
**
47888 AATTATTG
1 AAGAATTG
47896 -A-AATTG
1 AAGAATTG
* *
47902 GAGCATTG
1 AAGAATTG
*
47910 AAGAACTG
1 AAGAATTG
47918 --GAATTG
1 AAGAATTG
*
47924 AAGCATTG
1 AAGAATTG
*
47932 AAGTATTG
1 AAGAATTG
47940 --GAATTG
1 AAGAATTG
*
47946 AAGCATTG
1 AAGAATTG
47954 AAGAATTG
1 AAGAATTG
47962 -A-AATTG
1 AAGAATTG
*
47968 -A-AACTG
1 AAGAATTG
*
47974 AAGGATTG
1 AAGAATTG
47982 AAGAATTG
1 AAGAATTG
*
47990 -A-AATCG
1 AAGAATTG
*
47996 AAGCATTG
1 AAGAATTG
*
48004 AAGTATTG
1 AAGAATTG
48012 --GAATTG
1 AAGAATTG
*
48018 AAGCATTG
1 AAGAATTG
48026 AAGAATTG
1 AAGAATTG
48034 -A-AATTG
1 AAGAATTG
*
48040 AAGGATTG
1 AAGAATTG
*
48048 AAGTATTG
1 AAGAATTG
*
48056 -A-AACTG
1 AAGAATTG
*
48062 AATAATTG
1 AAGAATTG
*
48070 AAGCATTG
1 AAGAATTG
*
48078 AAGAGTTG
1 AAGAATTG
48086 -A-AATTG
1 AAGAATTG
*
48092 AAGTATTG
1 AAGAATTG
48100 AAGAATTG
1 AAGAATTG
*
48108 -A-AACTG
1 AAGAATTG
*
48114 AAGCATTG
1 AAGAATTG
*
48122 AAAAATTG
1 AAGAATTG
*
48130 --GAATCG
1 AAGAATTG
*
48136 AAGCATTG
1 AAGAATTG
*
48144 AAGTATTG
1 AAGAATTG
48152 --GAATTG
1 AAGAATTG
*
48158 AAGCATTG
1 AAGAATTG
*
48166 AAGTATTG
1 AAGAATTG
48174 -AG-ATTG
1 AAGAATTG
*
48180 AAGAATTA
1 AAGAATTG
48188 AAGAATTG
1 AAGAATTG
48196 -A-AATTG
1 AAGAATTG
* *
48202 AATAACTG
1 AAGAATTG
48210 AAGAATTG
1 AAGAATTG
48218 AA-AA-TG
1 AAGAATTG
*
48224 AAGTATTG
1 AAGAATTG
48232 AAGAATTG
1 AAGAATTG
*
48240 -A-AACTG
1 AAGAATTG
*
48246 AAGCATTG
1 AAGAATTG
*
48254 CAGAATTG
1 AAGAATTG
48262 -A-AATTG
1 AAGAATTG
* * *
48268 AATAACTA
1 AAGAATTG
48276 AAGAATTG
1 AAGAATTG
48284 -A-AATTG
1 AAGAATTG
*
48290 AA-ATATTA
1 AAGA-ATTG
48298 AATG-ATTG
1 AA-GAATTG
*
48306 -A-AATTA
1 AAGAATTG
* *
48312 AATAACTG
1 AAGAATTG
48320 AAGAATTG
1 AAGAATTG
48328 -A-AATTG
1 AAGAATTG
*
48334 AAGCATTG
1 AAGAATTG
*
48342 AAAAATTG
1 AAGAATTG
48350 -A-AATTG
1 AAGAATTG
48356 AA-ACATTG
1 AAGA-ATTG
*
48364 AAGATTTG
1 AAGAATTG
*
48372 -A-ATTTG
1 AAGAATTG
48378 AAGAATTG
1 AAGAATTG
48386 AA-ATATTG
1 AAGA-ATTG
48394 -A-AATTG
1 AAGAATTG
**
48400 AACCATTG
1 AAGAATTG
48408 AA-ATATTG
1 AAGA-ATTG
48416 AA-ATATTG
1 AAGA-ATTG
48424 -A-AATTG
1 AAGAATTG
48430 AA-ACATTG
1 AAGA-ATTG
*
48438 AAGATTTG
1 AAGAATTG
48446 AA
1 AA
48448 TTTTGGAAAA
Statistics
Matches: 536, Mismatches: 105, Indels: 122
0.70 0.14 0.16
Matches are distributed among these distances:
6 115 0.21
7 51 0.10
8 366 0.68
9 4 0.01
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29
Consensus pattern (8 bp):
AAGAATTG
Found at i:47762 original size:16 final size:16
Alignment explanation
Indices: 47738--48616 Score: 235
Period size: 14 Copynumber: 58.2 Consensus size: 16
47728 AATTGAAATA
47738 AAGAATTGAATAATTG
1 AAGAATTGAATAATTG
*
47754 AATAATTGAA-ACATTG
1 AAGAATTGAATA-ATTG
* * *
47770 AATAATTGAAGAGTTG
1 AAGAATTGAATAATTG
47786 AAGAATTGAATAATTG
1 AAGAATTGAATAATTG
* **
47802 GAGAATTGAAGCATTG
1 AAGAATTGAATAATTG
**
47818 AAGCGTTGAATAATTG
1 AAGAATTGAATAATTG
* * *
47834 AAGAACTGAATGACTG
1 AAGAATTGAATAATTG
* **
47850 AGGAATTGAAGCATTG
1 AAGAATTGAATAATTG
* *
47866 AATAATTG-A-ACTTG
1 AAGAATTGAATAATTG
* *
47880 AAGCATTGAATTATTG
1 AAGAATTGAATAATTG
* **
47896 -A-AATTGGAGCATTG
1 AAGAATTGAATAATTG
* *
47910 AAGAACTG--GAATTG
1 AAGAATTGAATAATTG
*
47924 AAGCATTGAAGT-ATTG
1 AAGAATTGAA-TAATTG
**
47940 --GAATTGAAGCATTG
1 AAGAATTGAATAATTG
47954 AAGAATTG-A-AATTG
1 AAGAATTGAATAATTG
* **
47968 -A-AACTGAAGGATTG
1 AAGAATTGAATAATTG
*
47982 AAGAATTG-A-AATCG
1 AAGAATTGAATAATTG
*
47996 AAGCATTGAAGT-ATTG
1 AAGAATTGAA-TAATTG
**
48012 --GAATTGAAGCATTG
1 AAGAATTGAATAATTG
48026 AAGAATTG-A-AATTG
1 AAGAATTGAATAATTG
*
48040 AAGGATTGAAGT-ATTG
1 AAGAATTGAA-TAATTG
*
48056 -A-AACTGAATAATTG
1 AAGAATTGAATAATTG
* * *
48070 AAGCATTGAAGAGTTG
1 AAGAATTGAATAATTG
48086 -A-AATTGAAGT-ATTG
1 AAGAATTGAA-TAATTG
*
48100 AAGAATTG-A-AACTG
1 AAGAATTGAATAATTG
* *
48114 AAGCATTGAAAAATTG
1 AAGAATTGAATAATTG
* **
48130 --GAATCGAAGCATTG
1 AAGAATTGAATAATTG
* *
48144 AAGTATTG--GAATTG
1 AAGAATTGAATAATTG
*
48158 AAGCATTGAAGT-ATTG
1 AAGAATTGAA-TAATTG
* *
48174 -AG-ATTGAAGAATTA
1 AAGAATTGAATAATTG
48188 AAGAATTG-A-AATTG
1 AAGAATTGAATAATTG
* * *
48202 AATAACTGAAGAATTG
1 AAGAATTGAATAATTG
48218 AA-AA-TGAAGT-ATTG
1 AAGAATTGAA-TAATTG
*
48232 AAGAATTG-A-AACTG
1 AAGAATTGAATAATTG
* * *
48246 AAGCATTGCAGAATTG
1 AAGAATTGAATAATTG
* *
48262 -A-AATTGAATAACTA
1 AAGAATTGAATAATTG
48276 AAGAATTG-A-AATTG
1 AAGAATTGAATAATTG
* *
48290 AA-ATATTAAATGATTG
1 AAGA-ATTGAATAATTG
* *
48306 -A-AATTAAATAACTG
1 AAGAATTGAATAATTG
48320 AAGAATTG-A-AATTG
1 AAGAATTGAATAATTG
* *
48334 AAGCATTGAAAAATTG
1 AAGAATTGAATAATTG
48350 -A-AATTGAA-ACATTG
1 AAGAATTGAATA-ATTG
*
48364 AAGATTTGAAT--TTG
1 AAGAATTGAATAATTG
48378 AAGAATTGAA-ATATTG
1 AAGAATTGAATA-ATTG
**
48394 -A-AATTGAACCATTG
1 AAGAATTGAATAATTG
48408 AA-ATATTGAA-ATATTG
1 AAGA-ATTGAATA-ATTG
48424 -A-AATTGAA-ACATTG
1 AAGAATTGAATA-ATTG
* *
48438 AAGATTTGAAT-TTTGG
1 AAGAATTGAATAATT-G
48454 AA-AATTGAA-ATATTG
1 AAGAATTGAATA-ATTG
* **
48469 -A-CACCGAA-ACATTG
1 AAGAATTGAATA-ATTG
48483 AA-AATTTG-ATATATTG
1 AAGAA-TTGAATA-ATTG
48499 -A-AATTGAA-ACATTG
1 AAGAATTGAATA-ATTG
* *
48513 AAGATTTGAAT-TTTG
1 AAGAATTGAATAATTG
48528 AAGAATTGAA-ATATTG
1 AAGAATTGAATA-ATTG
48544 AAATGGAAACATTGAGA-AATTG
1 -AA--G--A-ATTGA-ATAATTG
*
48566 AAGAATTGAAGAATTGG
1 AAGAATTGAATAATT-G
* *
48583 AA-CATTGGATAATTG
1 AAGAATTGAATAATTG
*
48598 AAGAATTGAAAAATTG
1 AAGAATTGAATAATTG
48614 AAG
1 AAG
48617 TTAATTGAAC
Statistics
Matches: 641, Mismatches: 127, Indels: 190
0.67 0.13 0.20
Matches are distributed among these distances:
12 4 0.01
13 5 0.01
14 268 0.42
15 79 0.12
16 262 0.41
17 7 0.01
19 2 0.00
21 3 0.00
22 9 0.01
23 2 0.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (16 bp):
AAGAATTGAATAATTG
Found at i:47772 original size:24 final size:24
Alignment explanation
Indices: 47742--48625 Score: 219
Period size: 22 Copynumber: 38.6 Consensus size: 24
47732 GAAATAAAGA
*
47742 ATTGAATAATTGAATAATTGAAAC
1 ATTGAATAATTGAAGAATTGAAAC
*
47766 ATTGAATAATTGAAGAGTTGAAGA-
1 ATTGAATAATTGAAGAATTGAA-AC
* *
47790 ATTGAATAATTGGAGAATTGAAGC
1 ATTGAATAATTGAAGAATTGAAAC
*** *
47814 ATTGAAGCGTTGAATAATTGAAGA-
1 ATTGAATAATTGAAGAATTGAA-AC
* * * * *
47838 ACTGAATGACTGAGGAATTGAAGC
1 ATTGAATAATTGAAGAATTGAAAC
* *
47862 ATTGAATAATTG-A-ACTTGAAGC
1 ATTGAATAATTGAAGAATTGAAAC
* * *
47884 ATTGAATTATTG-A-AATTGGAGC
1 ATTGAATAATTGAAGAATTGAAAC
* * *
47906 ATTGAAGAACTG--GAATTGAAGC
1 ATTGAATAATTGAAGAATTGAAAC
*
47928 ATTGAAGT-ATTG--GAATTGAAGC
1 ATTGAA-TAATTGAAGAATTGAAAC
*
47950 ATTGAAGAATTG-A-AATTGAAAC
1 ATTGAATAATTGAAGAATTGAAAC
**
47972 --TGAAGGATTGAAGAATTG-AA-
1 ATTGAATAATTGAAGAATTGAAAC
* ** * *
47992 ATCGAAGCATTGAAGTATTG-GA-
1 ATTGAATAATTGAAGAATTGAAAC
**
48014 ATTGAAGCATTGAAGAATTG-AA-
1 ATTGAATAATTGAAGAATTGAAAC
** *
48036 ATTGAAGGATTGAAGTATTGAAAC
1 ATTGAATAATTGAAGAATTGAAAC
*
48060 --TGAATAATTGAAGCATTGAAGA-
1 ATTGAATAATTGAAGAATTGAA-AC
* *
48082 GTTG-A-AATTGAAGTATTGAAGA-
1 ATTGAATAATTGAAGAATTGAA-AC
* * *
48104 ATTG-A-AACTGAAGCATTGAAAA
1 ATTGAATAATTGAAGAATTGAAAC
* *
48126 ATTGGAATCGAAGCATTGAAGTATTG-GA-
1 ATT-GAAT---A--ATTGAAGAATTGAAAC
** * *
48154 ATTGAAGCATTGAAGTATTG--AG
1 ATTGAATAATTGAAGAATTGAAAC
* *
48176 ATTGAAGAATTAAAGAATTG-AA-
1 ATTGAATAATTGAAGAATTGAAAC
*
48198 ATTGAATAACTGAAGAATTGAAA-
1 ATTGAATAATTGAAGAATTGAAAC
48221 A-TGAAGT-ATTGAAGAATTGAAAC
1 ATTGAA-TAATTGAAGAATTGAAAC
** *
48244 --TGAAGCATTGCAGAATTG-AA-
1 ATTGAATAATTGAAGAATTGAAAC
* *
48264 ATTGAATAACTAAAGAATTG-AA-
1 ATTGAATAATTGAAGAATTGAAAC
*
48286 ATTGAA-ATATTAAATG-ATTG-AA-
1 ATTGAATA-ATTGAA-GAATTGAAAC
* *
48308 ATTAAATAACTGAAGAATTG-AA-
1 ATTGAATAATTGAAGAATTGAAAC
** *
48330 ATTGAAGCATTGAAAAATTG-AA-
1 ATTGAATAATTGAAGAATTGAAAC
*
48352 ATTGAA-ACATTGAAGATTTG-AA-
1 ATTGAATA-ATTGAAGAATTGAAAC
* *
48374 TTTGAAGAATTGAA-ATATTG-AA-
1 ATTGAATAATTGAAGA-ATTGAAAC
** *
48396 ATTGAACCATTGAA-ATATTGAAAT
1 ATTGAATAATTGAAGA-ATTGAAAC
48420 ATTG-A-AATTGAA-ACATTGAAGA-
1 ATTGAATAATTGAAGA-ATTGAA-AC
* * *
48442 TTTGAAT-TTTGGAA-AATTGAAAT
1 ATTGAATAATT-GAAGAATTGAAAC
* **
48465 ATTG-A-CACCGAA-ACATTGAAA-
1 ATTGAATAATTGAAGA-ATTGAAAC
48486 ATTTG-ATATATTG-A-AATTGAAAC
1 A-TTGAATA-ATTGAAGAATTGAAAC
*
48509 ATTGAAGATTTGAATTTTGAAGAATTGAAAT
1 ATTG-A-A--T-AA--TTGAAGAATTGAAAC
*
48540 ATTG-A-AATGGAA-ACATTGAGAA-
1 ATTGAATAATTGAAGA-ATTGA-AAC
* *
48562 ATTGAAGAATTGAAGAATTGGAAC
1 ATTGAATAATTGAAGAATTGAAAC
* *
48586 ATTGGATAATTGAAGAATTGAAAA
1 ATTGAATAATTGAAGAATTGAAAC
48610 ATTGAAGTTAATTGAA
1 ATTGAA--TAATTGAA
48626 CATGATTAGC
Statistics
Matches: 680, Mismatches: 108, Indels: 142
0.73 0.12 0.15
Matches are distributed among these distances:
20 9 0.01
21 16 0.02
22 438 0.64
23 37 0.05
24 131 0.19
25 3 0.00
26 8 0.01
27 5 0.01
28 6 0.01
29 4 0.01
30 11 0.02
31 12 0.02
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.30
Consensus pattern (24 bp):
ATTGAATAATTGAAGAATTGAAAC
Found at i:47925 original size:44 final size:44
Alignment explanation
Indices: 47853--48409 Score: 456
Period size: 44 Copynumber: 12.3 Consensus size: 44
47843 ATGACTGAGG
* **
47853 AATTGAAGCATTGAATAATT-GAACTTGAAGCATTGAATTATTGA
1 AATTGAAGCATTGAAGAATTGGAA-TTGAAGCATTGAAGAATTGA
* * * *
47897 AATTGGAGCATTGAAGAACTGGAATTGAAGCATTGAAGTATTGG
1 AATTGAAGCATTGAAGAATTGGAATTGAAGCATTGAAGAATTGA
* *
47941 AATTGAAGCATTGAAGAATTGAAATTGAAACTGAAGGATTGAAGAATTGA
1 AATTGAAGCATTGAAGAATTG-----G-AATTGAAGCATTGAAGAATTGA
* *
47991 AATCGAAGCATTGAAGTATTGGAATTGAAGCATTGAAGAATTGA
1 AATTGAAGCATTGAAGAATTGGAATTGAAGCATTGAAGAATTGA
* * *
48035 AATTGAAGGATTGAAGTATTGAAACTGAATAATTGAAGCATTGAAGAGTTGA
1 AATTGAAGCATTGAAGAATTG-----G---AATTGAAGCATTGAAGAATTGA
* * * * *
48087 AATTGAAGTATTGAAGAATTGAAACTGAAGCATTGAAAAATTGG
1 AATTGAAGCATTGAAGAATTGGAATTGAAGCATTGAAGAATTGA
* * *
48131 AATCGAAGCATTGAAGTATTGGAATTGAAGCATTGAAGTATTGA
1 AATTGAAGCATTGAAGAATTGGAATTGAAGCATTGAAGAATTGA
* * * * ** *
48175 GATTGAAGAATTAAAGAATTGAAATTGAATAACTGAAGAATTGA
1 AATTGAAGCATTGAAGAATTGGAATTGAAGCATTGAAGAATTGA
* * * * *
48219 AAATGAAGTATTGAAGAATTGAAACTGAAGCATTGCAGAATTGA
1 AATTGAAGCATTGAAGAATTGGAATTGAAGCATTGAAGAATTGA
** * * * ** *
48263 AATTGAATAACTAAAGAATTGAAATTGAAATATTAAATG-ATTGA
1 AATTGAAGCATTGAAGAATTGGAATTGAAGCATTGAA-GAATTGA
* ** * * *
48307 AATTAAATAACTGAAGAATTGAAATTGAAGCATTGAAAAATTGA
1 AATTGAAGCATTGAAGAATTGGAATTGAAGCATTGAAGAATTGA
* * *
48351 AATTGAAACATTGAAG-ATTTGAATTTGAAGAATTGAA-ATATTGA
1 AATTGAAGCATTGAAGAATTGGAA-TTGAAGCATTGAAGA-ATTGA
*
48395 AATTGAACCATTGAA
1 AATTGAAGCATTGAA
48410 ATATTGAAAT
Statistics
Matches: 418, Mismatches: 76, Indels: 38
0.79 0.14 0.07
Matches are distributed among these distances:
43 6 0.01
44 328 0.78
45 5 0.01
49 2 0.00
50 37 0.09
52 40 0.10
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29
Consensus pattern (44 bp):
AATTGAAGCATTGAAGAATTGGAATTGAAGCATTGAAGAATTGA
Found at i:47947 original size:66 final size:66
Alignment explanation
Indices: 47729--48419 Score: 514
Period size: 66 Copynumber: 10.1 Consensus size: 66
47719 CCCTGGATCA
* * * * * *
47729 ATTGAAA-TAAAGAATTGAATAATTGAATAATTGAAACATTGAATAATTGAAGAGTTGAAGAATT
1 ATTGAAATTGAAGCATTGAAGAATTG-A-AATTGAAGCATTGAAGAATTGAA-A-TTGAAGCATT
47793 GAA-T
62 GAAGT
** * * *
47797 AATTGGAGAATTGAAGCATTGAAGCGTTGAATAATTGAAGAACTGAATG-ACTGAGGAATTGAAG
1 -ATT-GA-AATTGAAGCATTGAAGAATTG-A-AATTGAAGCATTGAA-GAATTGA--AATTGAAG
47861 CATTGAA-T
58 CATTGAAGT
* ** * * *
47869 AATTGAACTTGAAGCATTGAATTATTGAAATTGGAGCATTGAAGAACTGGAATTGAAGCATTGAA
1 -ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAA
47934 GT
65 GT
* * *
47936 ATTGGAATTGAAGCATTGAAGAATTGAAATTGAAACTGAAGGATTGAAGAATTGAAATCGAAGCA
1 ATTGAAATTGAAGCATTGAAGAATTGAAA-T-----TGAAGCATTGAAGAATTGAAATTGAAGCA
48001 TTGAAGT
60 TTGAAGT
* * *
48008 ATTGGAATTGAAGCATTGAAGAATTGAAATTGAAGGATTGAAGTATTGAAACTGAATAATTGAAG
1 ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTG-A--A--G-AATTG-A-AATTGAAG
48073 CATTGAAG-
58 CATTGAAGT
* * * * *
48081 AGTTGAAATTGAAGTATTGAAGAATTGAAACTGAAGCATTGAAAAATTGGAATCGAAGCATTGAA
1 A-TTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAA
48146 GT
65 GT
* * * * * ** *
48148 ATTGGAATTGAAGCATTGAAGTATTGAGATTGAAGAATTAAAGAATTGAAATTGAATAACTGAAG
1 ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAG
*
48213 A
66 T
* * * * ** * *
48214 ATTGAAAATGAAGTATTGAAGAATTGAAACTGAAGCATTGCAGAATTGAAATTGAATAACTAAAG
1 ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAG
*
48279 A
66 T
** * * ** *
48280 ATTGAAATTGAAATATTAAATG-ATTGAAATTAAATAACTGAAGAATTGAAATTGAAGCATTGAA
1 ATTGAAATTGAAGCATTGAA-GAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAA
**
48344 AA
65 GT
* * * * *
48346 ATTGAAATTGAAACATTGAAGATTTGAATTTGAAGAATTGAA-ATATTGAAATTGAACCATTGAA
1 ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGA-ATTGAAATTGAAGCATTGAA
*
48410 AT
65 GT
48412 ATTGAAAT
1 ATTGAAAT
48420 ATTGAAATTG
Statistics
Matches: 510, Mismatches: 85, Indels: 57
0.78 0.13 0.09
Matches are distributed among these distances:
65 2 0.00
66 283 0.55
67 6 0.01
68 20 0.04
69 5 0.01
70 19 0.04
71 7 0.01
72 113 0.22
73 4 0.01
74 51 0.10
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29
Consensus pattern (66 bp):
ATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAG
T
Found at i:48232 original size:52 final size:51
Alignment explanation
Indices: 48014--48238 Score: 161
Period size: 52 Copynumber: 4.2 Consensus size: 51
48004 AAGTATTGGA
* * * *
48014 ATTGAAGCATTGAAGAATTGAAATTGAAGGATTGAAGTATTGAAACTGAA-T
1 ATTGAAGAATTAAAGAATTGAAATTGAA-TATTGAAGAATTGAAACTGAAGT
* * * *
48065 AATTGAAGCATTGAAGAGTTGAAATTGAAGTATTGAAGAATTGAAACTGAAGC
1 -ATTGAAGAATTAAAGAATTGAAATTGAA-TATTGAAGAATTGAAACTGAAGT
* * * * *
48118 ATTGAAAAATTGGAATCGAAGCATTGAAGTATTGGA-ATTGAAGCATTGAAGTATTG-AG-
1 ATTGAAGAATT---A---AAGAATTGAA--ATTGAATATTGAAGAATTGAA--ACTGAAGT
* *
48176 ATTGAAGAATTAAAGAATTGAAATTGAATAACTGAAGAATTGAAAATGAAGT
1 ATTGAAGAATTAAAGAATTGAAATTGAAT-ATTGAAGAATTGAAACTGAAGT
48228 ATTGAAGAATT
1 ATTGAAGAATT
48239 GAAACTGAAG
Statistics
Matches: 140, Mismatches: 18, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
50 8 0.06
51 2 0.01
52 88 0.63
55 1 0.01
58 31 0.22
59 2 0.01
60 8 0.06
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.28
Consensus pattern (51 bp):
ATTGAAGAATTAAAGAATTGAAATTGAATATTGAAGAATTGAAACTGAAGT
Found at i:48366 original size:30 final size:28
Alignment explanation
Indices: 48338--48575 Score: 99
Period size: 30 Copynumber: 8.0 Consensus size: 28
48328 AAATTGAAGC
48338 ATTGAAAAATTGAAATTGAAACATTGAA
1 ATTGAAAAATTGAAATTGAAACATTGAA
* *
48366 GATTTG--AATTTGAAGAATTGAAATATTGAA
1 -A-TTGAAAAATTG-A-AATTGAAACATTGAA
** *
48396 ATTGAACCATTGAAATATTGAAATATTGAA
1 ATTGAAAAATTG-AA-ATTGAAACATTGAA
* **
48426 ATTGAAACATTGAAGATTTG-AATTTTGGAAA
1 ATTGAAAAATTGAA-A-TTGAAACATT-G-AA
* * **
48457 ATTGAAATATTGACACCGAAACATTGAAA
1 ATTGAAAAATTGAAATTGAAACATTG-AA
* *
48486 ATTTGATATATTGAAATTGAAACATTGAA
1 A-TTGAAAAATTGAAATTGAAACATTGAA
** *
48515 GATTTG-AATTTTGAAGAATTGAAATATTGAA
1 -A-TTGAAAAATTG-A-AATTGAAACATTGAA
* *
48546 ATGGAAACATTGAGAAATTGAAGA-ATTGAA
1 ATTGAAAAATT--GAAATTGAA-ACATTGAA
48576 GAATTGGAAC
Statistics
Matches: 167, Mismatches: 24, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
28 8 0.05
29 27 0.16
30 101 0.60
31 30 0.18
32 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.32
Consensus pattern (28 bp):
ATTGAAAAATTGAAATTGAAACATTGAA
Found at i:48478 original size:45 final size:45
Alignment explanation
Indices: 48404--48514 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 45
48394 AAATTGAACC
** *
48404 ATTGAAATATTGAAATATTGAAATTGAAACATTGAAGATTTGA-AT
1 ATTGAAA-ATTGAAATATTGAAACCGAAACATTGAAAATTTGATAT
* *
48449 TTTGGAAAATTGAAATATTGACACCGAAACATTGAAAATTTGATAT
1 ATT-GAAAATTGAAATATTGAAACCGAAACATTGAAAATTTGATAT
*
48495 ATTG-AAATTGAAACATTGAA
1 ATTGAAAATTGAAATATTGAA
48515 GATTTGAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
44 14 0.25
45 34 0.61
46 8 0.14
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (45 bp):
ATTGAAAATTGAAATATTGAAACCGAAACATTGAAAATTTGATAT
Found at i:48485 original size:8 final size:7
Alignment explanation
Indices: 48176--48615 Score: 145
Period size: 8 Copynumber: 58.9 Consensus size: 7
48166 AAGTATTGAG
48176 ATTGAAGA
1 ATTGAA-A
*
48184 ATTAAAGA
1 ATTGAA-A
48192 ATTG-AA
1 ATTGAAA
48198 ATTGAATA
1 ATTGAA-A
*
48206 ACTGAAGA
1 ATTGAA-A
48214 ATTGAAA
1 ATTGAAA
*
48221 A-TGAAGT
1 ATTGAA-A
48228 ATTGAAGA
1 ATTGAA-A
48236 ATTG-AA
1 ATTGAAA
* *
48242 ACTGAAGC
1 ATTGAA-A
*
48250 ATTGCAGA
1 ATTG-AAA
48258 ATTG-AA
1 ATTGAAA
48264 ATTGAATA
1 ATTGAA-A
* *
48272 ACTAAAGA
1 ATTGAA-A
48280 ATTG-AA
1 ATTGAAA
48286 ATTGAAA
1 ATTGAAA
48293 TATT-AAA
1 -ATTGAAA
48300 TGATTG-AA
1 --ATTGAAA
*
48308 ATTAAATA
1 ATTGAA-A
*
48316 ACTGAAGA
1 ATTGAA-A
48324 ATTG-AA
1 ATTGAAA
*
48330 ATTGAAGC
1 ATTGAA-A
48338 ATTGAAAA
1 ATTG-AAA
48346 ATTG-AA
1 ATTGAAA
48352 ATTGAAA
1 ATTGAAA
48359 CATTGAAGA
1 -ATTGAA-A
*
48368 TTTG-AA
1 ATTGAAA
*
48374 TTTGAAGA
1 ATTGAA-A
48382 ATTGAAA
1 ATTGAAA
48389 TATTG-AA
1 -ATTGAAA
*
48396 ATTGAACC
1 ATTGAA-A
48404 ATTGAAA
1 ATTGAAA
48411 TATTGAAA
1 -ATTGAAA
48419 TATTG-AA
1 -ATTGAAA
48426 ATTGAAA
1 ATTGAAA
48433 CATTGAAGA
1 -ATTGAA-A
* *
48442 TTTGAAT
1 ATTGAAA
*
48449 TTTGGAAA
1 ATT-GAAA
48457 ATTGAAA
1 ATTGAAA
*
48464 TATTG-AC
1 -ATTGAAA
**
48471 ACCGAAA
1 ATTGAAA
48478 CATTGAAA
1 -ATTGAAA
*
48486 ATTTGATAT
1 A-TTGA-AA
48495 ATTG-AA
1 ATTGAAA
48501 ATTGAAA
1 ATTGAAA
48508 CATTGAAGA
1 -ATTGAA-A
* *
48517 TTTGAAT
1 ATTGAAA
*
48524 TTTGAAGA
1 ATTGAA-A
48532 ATTGAAA
1 ATTGAAA
48539 TATTG-AA
1 -ATTGAAA
*
48546 ATGGAAA
1 ATTGAAA
48553 CATTGAGAA
1 -ATTGA-AA
48562 ATTGAAGA
1 ATTGAA-A
48570 ATTGAAGA
1 ATTGAA-A
*
48578 ATTGGAAC
1 ATT-GAAA
*
48586 ATTGGATA
1 ATT-GAAA
48594 ATTGAAGA
1 ATTGAA-A
48602 ATTGAAAA
1 ATTG-AAA
48610 ATTGAA
1 ATTGAA
48616 GTTAATTGAA
Statistics
Matches: 332, Mismatches: 52, Indels: 97
0.69 0.11 0.20
Matches are distributed among these distances:
6 60 0.18
7 57 0.17
8 200 0.60
9 15 0.05
ACGTcount: A:0.48, C:0.04, G:0.18, T:0.30
Consensus pattern (7 bp):
ATTGAAA
Found at i:48501 original size:75 final size:75
Alignment explanation
Indices: 48339--48589 Score: 341
Period size: 75 Copynumber: 3.3 Consensus size: 75
48329 AATTGAAGCA
* * *
48339 TTGAAAAATTGAAATTGAAACATTGAAGATTTGAA-TTTGAAGAATTGAAATATTGAAATTGAAC
1 TTGAAATATTGAAATTGAAACATTGAAGATTTGAATTTTGAAGAATTGAAATATTGAAATCGAAA
48403 CATTG-AAAT
66 CATTGAAAAT
* *
48412 ATTGAAATATTGAAATTGAAACATTGAAGATTTGAATTTTGGAA-AATTGAAATATTGACACCGA
1 -TTGAAATATTGAAATTGAAACATTGAAGATTTGAATTTT-GAAGAATTGAAATATTGAAATCGA
48476 AACATTGAAAAT
64 AACATTGAAAAT
* *
48488 TTGATATATTGAAATTGAAACATTGAAGATTTGAATTTTGAAGAATTGAAATATTGAAATGGAAA
1 TTGAAATATTGAAATTGAAACATTGAAGATTTGAATTTTGAAGAATTGAAATATTGAAATCGAAA
48553 CATTGAGAAA-
66 CATTGA-AAAT
*
48563 TTGAAGA-ATTGAAGAATTGGAACATTG
1 TTGAA-ATATTG-A-AATTGAAACATTG
48590 GATAATTGAA
Statistics
Matches: 158, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
74 37 0.23
75 97 0.61
76 12 0.08
77 12 0.08
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.32
Consensus pattern (75 bp):
TTGAAATATTGAAATTGAAACATTGAAGATTTGAATTTTGAAGAATTGAAATATTGAAATCGAAA
CATTGAAAAT
Found at i:48567 original size:45 final size:46
Alignment explanation
Indices: 48479--48625 Score: 122
Period size: 45 Copynumber: 3.1 Consensus size: 46
48469 ACACCGAAAC
* * * *
48479 ATTGAA-AATTTGATATATTGAAATTGAAACATTGAAGATTTGAA-T
1 ATTGAAGAA-TTGAAATATTGAAATGGAAACATTGAAGAATTGAAGA
*
48524 TTTGAAGAATTGAAATATTGAAATGGAAACATTG-AGAAATTGAAGA
1 ATTGAAGAATTGAAATATTGAAATGGAAACATTGAAG-AATTGAAGA
* * * *
48570 ATTGAAGAATTGGAACATTGGATAATTGAAGA-ATTGAAAAATTGAAGTTA
1 ATTGAAGAATTGAAATATT-GA-AATGGAA-ACATTGAAGAATTGAAG--A
48620 ATTGAA
1 ATTGAA
48626 CATGATTAGC
Statistics
Matches: 83, Mismatches: 10, Indels: 13
0.78 0.09 0.12
Matches are distributed among these distances:
44 2 0.02
45 34 0.41
46 18 0.22
47 2 0.02
48 18 0.22
49 2 0.02
50 7 0.08
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (46 bp):
ATTGAAGAATTGAAATATTGAAATGGAAACATTGAAGAATTGAAGA
Done.