Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020511.1 Corchorus olitorius cultivar O-4 contig20544, 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: 21944
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Found at i:642 original size:27 final size:28
Alignment explanation
Indices: 603--675 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
593 TAAAATGCCC
*
603 AAAATGACCAAAATGCCCCT-GA-ATATG
1 AAAATGACCAAAATGCCCCTAGATATA-A
* *
630 CAAATGACTAAAATGCCCCTAGATATAA
1 AAAATGACCAAAATGCCCCTAGATATAA
658 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
676 TTGGGTCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 18 0.46
28 18 0.46
29 3 0.08
ACGTcount: A:0.47, C:0.23, G:0.12, T:0.18
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAGATATAA
Found at i:1462 original size:65 final size:65
Alignment explanation
Indices: 1352--1481 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
1342 GGAAAAACTG
* *
1352 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCACGCCAGGGCTAGTGCAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCAGGGCTAGTGCAGAAAGTTGGAATC
* *
1417 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCCTGGGCTAGTGCAGAAAGTTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCAGGGCTAGTGCAGAAAGTTGGAATC
1482 AATAACAAGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCAGGGCTAGTGCAGAAAGTTGGAATC
Found at i:1648 original size:21 final size:21
Alignment explanation
Indices: 1624--1667 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1614 TCCTGCTCTT
* *
1624 TTCATTGGACCTAATGGCATC
1 TTCAATGGACCAAATGGCATC
*
1645 TTCAATGGATCAAATGGCATC
1 TTCAATGGACCAAATGGCATC
1666 TT
1 TT
1668 AGGCAACTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (21 bp):
TTCAATGGACCAAATGGCATC
Found at i:3579 original size:33 final size:33
Alignment explanation
Indices: 3542--3646 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
3532 ATTAGCATCC
*
3542 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTATCATCACAAACAACACCT
* *
3575 AAAACAGATTTAGTGTCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
** * * *
3608 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
3641 AAAACA
1 AAAACA
3647 CTCTTTGCAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 4 0.07
33 56 0.93
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACCT
Found at i:5880 original size:20 final size:20
Alignment explanation
Indices: 5857--5895 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5847 TCTAAGGTAG
5857 AATTA-AACCCACAATGGCCA
1 AATTACAACCC-CAATGGCCA
*
5877 AATTACAACTCCAATGGCC
1 AATTACAACCCCAATGGCC
5896 TAATACTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.31, G:0.10, T:0.18
Consensus pattern (20 bp):
AATTACAACCCCAATGGCCA
Found at i:6138 original size:21 final size:21
Alignment explanation
Indices: 6114--6177 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
6104 CCTTAGGCAA
6114 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
6135 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
6156 CTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
6176 CT
1 CT
6178 TTGTGTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 37 0.90
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:7013 original size:65 final size:65
Alignment explanation
Indices: 6903--7032 Score: 208
Period size: 65 Copynumber: 2.0 Consensus size: 65
6893 GGAAAAACTG
*
6903 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCACACCAGGGCTAGTGCAGAAAGTTT-GAAT
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACACCAGGGCTAGTGCAGAAA-TTTGGAAT
6967 C
65 C
* * *
6968 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTTCAGAAATTTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACACCAGGGCTAGTGCAGAAATTTGGAATC
7033 AATAGCAAGC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 3 0.05
65 57 0.95
ACGTcount: A:0.22, C:0.31, G:0.25, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACACCAGGGCTAGTGCAGAAATTTGGAATC
Found at i:11550 original size:67 final size:66
Alignment explanation
Indices: 11385--11676 Score: 423
Period size: 67 Copynumber: 4.4 Consensus size: 66
11375 TTAAAGTTTT
* * *
11385 ATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTATTGCATTTAAGTTT-
1 ATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTTA
*
11449 T
66 C
*
11450 ATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGACATTTTTGTCTTTTTGCATTTGAGTTTA
1 ATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTTA
11515 GC
66 -C
* *
11517 ATTTTCACTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCT-TCTTTTTTCATTTGAGTTT
1 ATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTT-TGTCTTTTTGCATTTGAGTTT
11581 AGC
65 A-C
*
11584 -TTTTGCATTTCCAAAAATACCATTTCGGTCGAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTT
1 ATTTT-CATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTT
11648 AC
65 AC
* *
11650 -TTTTGATTACC-AAAATACCCTTTCGGT
1 ATTTTCATTTCCAAAAATACCCTTTCGGT
11677 GAAAAGGTCA
Statistics
Matches: 208, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
64 15 0.07
65 65 0.31
66 10 0.05
67 117 0.56
68 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (66 bp):
ATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTTGTCTTTTTGCATTTGAGTTTA
C
Found at i:13222 original size:154 final size:153
Alignment explanation
Indices: 12880--19940 Score: 6132
Period size: 154 Copynumber: 45.4 Consensus size: 153
12870 AAACCTCAAT
* * * *
12880 GGCCCCGATAGACCCAAAATAACAAGTGTTTCAAATGAGCTAAAAACATCACAGTGAACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
*
12945 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCC----C-AA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCCAAATCGAA
*
13005 AACGATTCAAAACGGAACTAATG
131 GACGATTCAAAACGGAACTAATG
* * * *
13028 GGCCCTGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGAGTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * *
13093 CACCATAATGATTACAGTTAGGCCATAAACAATGGAAATAAAAGCATCGATGGTTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTGCCAAATCGA
*
13158 AGACGATTCAAAACAGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
*
13182 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTATTCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * *
13247 CACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAGGTTTCCAAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCC-AAATCGA
* *
13312 AAACAATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
*
13336 AG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * * *
13400 CACCAAAATGATTATAGTTAGGCCATAAATAATGGAAGGAAAAGAATTGAGGGTTGTCAAGTCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTGCCAAATCGA
* *
13465 AGACGATTCAAAATGGAACTAGTG
130 AGACGATTCAAAACGGAACTAATG
**
13489 GG-CCCGATAGGCCCAAAATAACAAGTGTTAGAAATGAGCTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * *
13553 CACCAAAATGATTATAGTTAGGCCATAATCAATGAAAAGAAAAGCATTGAGATTTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-GTTGCCAAATCGA
*** *
13618 AGACGATTCAAAACTTCACTAAAG
130 AGACGATTCAAAACGGAACTAATG
* * *
13642 GG-CCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGGTAAAAACTTCACAGTGGACTAAACT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * *
13706 CACCAAAATTATTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
*
13771 AGACGATTCAAAACGGAATTAATG
130 AGACGATTCAAAACGGAACTAATG
* * * **
13795 GGCCCCGATATGCCTAAAATAACAAGTCTTCCAAATGAATTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * *
13860 CACCCAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATCGAGGGATGCCAAATCAA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTGCCAAATCGA
*
13924 AGACAATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * *
13948 TGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACTGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * * *
14013 TACTAAAATGATTATAATTAGGTCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCTAAAT-GA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCC-AAATCG-
*
14077 AAGACGATTCAAAATGGAACTAATG
129 AAGACGATTCAAAACGGAACTAATG
* * * * *
14102 GGCCCCGATAGGCCCAAGATAACAAGTGTTCCAAATGTGTTTAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * * *
14167 CACCATAATGATTACAATTAGGCAATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
* *
14232 AGACGATTCAAAATGGATCTAATG
130 AGACGATTCAAAACGGAACTAATG
* * * *
14256 GGTCCTGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATGT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* *
14321 CACCAAAATGATTATAGTTAGGCCATACACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
*
14386 AGACGATTCAAAACGAAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * * *
14410 AG-CCCGATAGGCCTAAAATAATAAGTGTTCCAAATGAG-TTAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
14473 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
* * *
14538 AGACTATTCAATACGTAACTAATG
130 AGACGATTCAAAACGGAACTAATG
** * *
14562 GGCTTCGATAGGCCC-AAATAACGAGTATTCC-AATGAGCT-AAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
*
14624 CACC-AAATGATTATAGTTAGGCCATAAA-AATGGAAAGAAAAGCATTGAGGTTTGCCAAACCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
14687 AGACGATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * ** * * *
14711 GGCGCCGATAGGCCCAAAATAACAGGTGTTCCACGTGATCTATAAAGTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* *
14776 CACCAAAATCATTATAGTTTGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
14841 AGACGATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * * * *
14865 AGCCCTGAAAGGCCCAAAATAACAAGTCTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * *
14930 CACCCAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATCGAGGGATGCCAAATCAA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTGCCAAATCGA
14994 AGACGATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * *
15018 GGCCCCGAAAGACCCAAAATAACAAGTGTTTCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * * *
15083 TACTAAAATGATTATAATTAGGTCATAAACAATGGAAA-AAAAGCATTGAGGTTTCC----C--A
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCCAAATCGAA
15141 -A--A-TCAAAAACGGAACTAATG
131 GACGATTC-AAAACGGAACTAATG
* * * * *
15161 GGCCCCGTTAGGCCCAAGATAATAAGTGTTCCAAATGAGCTTAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * * * *
15226 CACCATAATGATTACAATTAGGCAAT-ATCAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
*
15290 AGACGATTCAAAACGGATCTAATG
130 AGACGATTCAAAACGGAACTAATG
* * * * * *
15314 GGTCCTGATAGGTCCAAAATAACAAGTCTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATGT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * *
15379 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGTTTCCCAAACCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTGCCAAATCGA
* *
15444 AGACTATTTAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * * *
15468 AG-CCCGATAGGCCTAAAATAATAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCA
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * *
15532 CACCAAAATGATTATAGTTAGGCCATAATCAATGGAATGAAAAGCATTGAGCTTTCCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-GTTGCCAAATCGA
* * **
15597 AAACGATTCAAAATGTCACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * * * *
15621 GGCTCCGATAGGCCCAAAGTAACAAGTGTACCAAATGAGTTAAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * * * *
15686 CACCATAATGATTACAGTTAGGCAATAAACAATGGAAGGAAAAGAATTGAGGTTTGCCAAGTCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
**
15751 AGACGATTCAAAACGGAACTTGTG
130 AGACGATTCAAAACGGAACTAATG
15775 GG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* *
15839 CACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGTTTGCCAAATCGAA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCCAAATCGAA
*** *
15904 GACGATTCAAAACTTCACTAAAG
131 GACGATTCAAAACGGAACTAATG
* *
15927 GG-CCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * *
15991 CACCAAAATTATTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGGTTTCCTAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCC-AAATCGA
16056 AGACGATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * *
16080 GGCCCCGATATGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATGT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * * *
16145 CACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAAAAAAGAATTG-GTGTTTTCTAAATCG
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-G-TTGCCAAATCG
16209 AAGACGATTCAAAACGGAACTAATG
129 AAGACGATTCAAAACGGAACTAATG
* * * *
16234 GGCCCCGAAAGACCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * *
16299 CACCATAATGATTATAGTTAGGCCATAATCAATGGAAAGAAAAGAATTGAAGTTTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-AGGTTGCCAAATCGA
***
16364 AGACGATTCAAAACTTCACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * * * *
16388 GG-CCCGTTAGGCCAAAAATAACAAATGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAACCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * *
16452 CACCAAAATTATTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATAT-AGGTTTTCCAAATCG
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-TGAGG-TTGCCAAATCG
16516 AAGACGATTCAAAACGGAACTAATG
129 AAGACGATTCAAAACGGAACTAATG
* * * *
16541 GGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAATTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
** * * * *
16606 CACCGTAATGATTACAATTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTACCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
* *
16671 AGACGATTCAAAATGGATCTAATG
130 AGACGATTCAAAACGGAACTAATG
** ** * *
16695 GGCCCTAATAGTTCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAGT-T
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
** * * *** *
16759 -AGGCCATACACAATGGAAAGAAAAGCATTGAGGTTTCCCA-AATCGAA-GACGATTCAAAACGG
66 CA--CC--A-A-AAT-G--ATTATAG--TT-AGG----CCATAAAC-AATG--GAAAGAAAA-GC
*** * * ** *
16821 AACTA-ATGGGCC----CGATAG--GCCT-AAAA--TAAC-AA-G
111 ATTGAGGT-TGCCAAATCGA-AGACGATTCAAAACGGAACTAATG
** ** * *** * ** * * * * * *
16854 TGTTCCAAATAAGTTAAAAACTTCACAA-TGGACTAATCTCA-CCAAAATGA-TT-ATAGTTAGA
1 -GGCCCCGATAGGCCCAAAA--TAACAAGTGTTCCAA-ATGAGCTAAAA--ACTTCACAG-TGGA
* * * * ** * ***
16915 CCATAATCAATGGA-AAGAAAAGCATT-GAGCTT-TCCCA-AATCGAA-GACGATTCAAAATGTC
59 -C-TAATC--T-CACCA-AAATG-ATTATAG-TTAGGCCATAAAC-AATG--GAAAGAAAA-G-C
* * * **
16975 ACTAATGAGCTCCGATAGGCCCAAAGTAAC-AAG-TG-TTCAAAATGAGTTAAAAACTTCTCAG
111 A-T--TGAG----G-T-TG-CCAAA-T--CGAAGACGATTCAAAACG-G-----AACTAAT--G
* ** ** ** * * * ** *
17036 TGG-ACTAAT-CTCACCAAAATGATTATAGT-TAGGCCATAAATAATG-GAAGGAAA--AGA-AT
1 -GGCCCCGATAGGC-CCAAAAT-AACA-AGTGT--TCC--AAATGA-GCTAA--AAACTTCACAG
** * * * * * * * *
17094 TGAGGGT--TGTCAAGTCGAAGACGATTCAAAATGTCACTAATGGGC-T--CCGATAGGCCCAAA
55 TG-GACTAATCTC-A--CCAAAATGATT--ATA-GT---T-A-GGCCATAAACAAT-GG---AAA
* * ** **
17154 G-TAA-CA---A-GTGTACCAAAT-G-AGTTAAAAACTTCAAAGTGG-ACTAAT-
104 GAAAAGCATTGAGGT-TGCCAAATCGAAG---ACGA-TTCAAAACGGAACTAATG
** * *** **** * * ** ***
17199 CTCACC-ATAATGATTACAGTTAGGCAATAAACAA-TGGAAGGAAAAGA-ATTGAGGTTTGC-CA
1 GGCCCCGAT-A-G-GCCCA---A---AAT-AACAAGT-GTTCCAAATGAGCTAAAAACTT-CAC-
* * ** *** * * * * *
17260 AGTCGAAGACGATTCAAAACGGGTAATAACTTCGTA-CTA-GCCATACATTACTTACGGAAGTTA
53 AGT-G--GACTAATC-TCAC-CAAAATGA-TT-ATAGTTAGGCCATA-A--AC-AATGG-A---A
* * *** * * *
17323 TACGATCACCAAAATG-ATT-ATAGTTAGGCCATAAAC-AATG--GAAAGAAAA--GCATTGA-G
103 -A-G------AAAA-GCATTGA-GGTT--GCCA-AATCGAA-GACGATTCAAAACGGAACTAATG
* ** * * ** * * *
17380 GTTTGCCAAATCGA-AGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGA-CCAAAATA-AT-
1 G---GCC---CCGATAG--G-CCCAAAA--TAAC-AA-GTGTTCC-AAATGAGCTAAAA-ACTTC
** * * * * * * * * *
17441 A-AGTGTTCCAA-ATGATCTAAAA--ACTTCACA---AAGCCCTAATC--T---CAGCAAAATG-
51 ACAGTGGACTAATCTCA-CCAAAATGA-TT-ATAGTTAGGCCATAAACAATGGAAAG-AAAA-GC
* * *** * * *
17493 ATT-ATAGTTAGGCCATAAAC-AATG--GAAAGAAAA-GCATCGAGGAT-
111 ATTGA-GGTT--GCCA-AATCGAA-GACGATTCAAAACGGAACTA--ATG
* * ** * ** *
17537 TGCCAAATCGA-AGACGATTCAAAACGGAACTAA-TGGACCCCGAAA-G-GC-AAAAA--TAACA
1 GGCC---CCGATAG--G-CCCAAAA--TAAC-AAGT-G-TTCC-AAATGAGCTAAAAACTTCAC-
** * * * * * * * ** ** **
17595 AGTGTTCCAA-ATGAGCTTAAAA-CATCAAAGTCGACTAATCTCACCAA-AAT-GATTATAGTTA
53 AGTGGACTAATCTCA-C-CAAAATGATTATAGT----TAGGC-CATAAACAATGGA--A-AGAAA
* ** * * ** ** * * * * *
17656 GGCCATAAACAGTGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGATGATTCAAAACAAAACA
108 AG-CATTGA-GGTTGCCA-AATCG-A-AGACGATT--C-AA--AACG--G-----------AACT
*
17721 AAAG
150 AATG
* * * * *
17725 GACCCCAATAGGTCCAAAATAAAAAGTGTTTCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
*
17790 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTGAGGTTTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
**
17855 AGACGATTCAAAACGTCACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * *
17879 GGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATGT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * *
17944 CACCAAAATGGTTATAGTTAGGCCATACACAATGGAAAGAAAAGCATTGAGGTTTGGCAAATTGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
**
18009 AGACGATTCAAAACATAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* *
18033 GGCCCCGAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * *
18098 CACCAAAATGATTATAGTTAGGCCATAAACAAACAATTGAAAAAAAAAAGCATTGGGGTTTACCA
66 CACCAAAATGATTATAGTTAGGCCAT----AAACAA-TG-GAAAGAAAAGCATTGAGG-TTGCCA
*
18163 AATCGAAGACGATTCAAAACAGAACTAATG
124 AATCGAAGACGATTCAAAACGGAACTAATG
* * *
18193 GGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTACAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * *
18258 CACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAAAAAAGAATTG-GTGTTTTCCAAATCG
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-G-TTGCCAAATCG
*
18322 AAGACGATTCAAAACAGAACTAATG
129 AAGACGATTCAAAACGGAACTAATG
* * *
18347 GGCCCCGAAAGGCCCAAAATAACAAGTCTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * * *
18412 CACCCAAATGATTATAGTTAGGCCATAAACATTGGAAAG-AAAGCATCGAGGGATGCCAAATCAA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTGCCAAATCGA
*
18476 AGACAATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * **
18500 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTTTACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * * * *
18565 TACTAAAATGATTATAATTAAGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCAA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
*
18630 AGACGATTCAAAATGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * * *
18654 GGCCCCGGTAGGCCCAAGATAACAAGTGTTCCAAATGAGCTTAAAACTTCACAATGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
*
18719 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGGCTT-CCAAATCG
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GG-TTGCCAAATCG
* *
18783 AAGACAATTCAAAACGGATCTAATG
129 AAGACGATTCAAAACGGAACTAATG
* * * *
18808 GG-CCCGATAGTCCAAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAAACT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* ** * *
18872 CACCAAACTTCTTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
18937 AGACGATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* *
18961 GG-CCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTACAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * *
19025 CACCAAAATTATTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGGTTTCCAAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCC-AAATCGA
*
19090 AAACGATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
*
19114 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* * * *
19179 CACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTAAGGTTTCTAAAATC-A
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGC-CAAATCGA
19243 AGACGATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* * *
19267 GGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAAGCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* ** * *
19332 CACCAAACTTCTTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTGCCAAATCGA
19397 AGACGATTCAAAACGGAACTAATG
130 AGACGATTCAAAACGGAACTAATG
* *
19421 GGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTACAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* *
19486 CACCAAAATTATTATAGTTAGGCCATAAACAATGGAAA-AAAAGCATTG-GTGTTTTCCAAATCG
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-G-TTGCCAAATCG
*
19549 AAGACGATTCAAAACAGAACTAATG
129 AAGACGATTCAAAACGGAACTAATG
* *
19574 GGCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* *
19639 CACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-AGTGTTTCCCAAATCG
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-G-TTGCCAAATCG
*
19703 AAGACGATTCAAAATGGAACTAATG
129 AAGACGATTCAAAACGGAACTAATG
* * *
19728 GGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGATCTAAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
* *
19793 CACCATAATGATTACT-GTTAGGCCATAAACAATGGAAAGAAAA-CATCGAGGGTTGCCAAATCG
66 CACCAAAATGATTA-TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTGCCAAATCG
* *
19856 AAGACGATTCAAAACAGATCTAATG
129 AAGACGATTCAAAACGGAACTAATG
* * * *
19881 GGCCCTGATAGGTCCAAAATAACAAGTGTTTCAATTGAGCTAAAAACTTCACAGTGGACT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
19941 GTAGACACTA
Statistics
Matches: 5758, Mismatches: 823, Indels: 659
0.80 0.11 0.09
Matches are distributed among these distances:
142 12 0.00
143 105 0.02
144 4 0.00
145 1 0.00
146 1 0.00
148 105 0.02
149 74 0.01
150 39 0.01
151 41 0.01
152 317 0.06
153 2064 0.36
154 2375 0.41
155 21 0.00
156 7 0.00
157 2 0.00
158 8 0.00
159 7 0.00
160 155 0.03
161 22 0.00
162 16 0.00
163 17 0.00
164 14 0.00
165 7 0.00
166 14 0.00
167 19 0.00
168 15 0.00
169 19 0.00
170 19 0.00
171 17 0.00
172 12 0.00
173 14 0.00
174 9 0.00
175 15 0.00
176 6 0.00
177 8 0.00
178 16 0.00
179 12 0.00
180 12 0.00
181 28 0.00
182 30 0.01
183 19 0.00
184 12 0.00
185 22 0.00
186 6 0.00
187 11 0.00
188 6 0.00
189 3 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (153 bp):
GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTGCCAAATCGAA
GACGATTCAAAACGGAACTAATG
Found at i:13999 original size:307 final size:308
Alignment explanation
Indices: 12880--17281 Score: 5857
Period size: 307 Copynumber: 14.5 Consensus size: 308
12870 AAACCTCAAT
* * * * *
12880 GGCCCCGATAGACCCAAAATAACAAGTGTTTCAAATGAGCTAAAAACATCACAGTGAACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
12945 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT-CC----C-A
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
* * *
13004 AAACGATTCAAAACGGAACTAATGGGCCCTGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* * * * * *
13069 AAAAACTTCAAAGTGGAGTAATCTCACCATAATGATTACAGTTAGGCCATAAACAATGGAAATAA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
* * *
13134 AAGCATCGATGG-TTGCCAAATCGAAGACGATTCAAAACAGAACTAATG
261 AAGCATTGA-GGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* *
13182 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTATTCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* *
13247 CACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTAAGGTTT-CCAAAATCG
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC-AAATCG
* * *
13311 AAAACAATTCAAAACGGAACTAATGAG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
130 AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
*
13375 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAT-AATGGAAGG
195 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT-AATCAATGGAAAG
* * * * *
13439 AAAAGAATTGAGGGTTGT-CAAGTCGAAGACGATTCAAAATGGAACTAGTG
259 AAAAGCATTGA-GGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
** *
13489 GG-CCCGATAGGCCCAAAATAACAAGTGTTAGAAATGAGCTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* * *
13553 CACCAAAATGATTATAGTTAGGCCATAATCAATGAAAAGAAAAGCATTGAGATTTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
*** * * *
13618 AGACGATTCAAAACTTCACTAAAGGG-CCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGGT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* *
13682 AAAAACTTCACAGTGGACTAAACTCACCAAAATTATTATAGTTAGGCCATAATCAATGGAAAGAA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
*
13747 AAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAATTAATG
261 AAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * * *
13795 GGCCCCGATATGCCTAAAATAACAAGTCTTCCAAATGAATTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* * ** *
13860 CACCCAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATCGAGGGATGCCAAATCAA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
* * *
13924 AGACAATTCAAAACGGAACTAATGTGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* * * * * *
13989 AAAAACTTCACTGTGGACTAATCTTACTAAAATGATTATAATTAGGTCATAAACAATGGAAAGAA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
*
14054 AAGCATTGAGG-TTTCCTAAAT-GAAAGACGATTCAAAATGGAACTAATG
261 AAGCATTGAGGTTTTCC-AAATCG-AAGACGATTCAAAACGGAACTAATG
* * * *
14102 GGCCCCGATAGGCCCAAGATAACAAGTGTTCCAAATGTGTTTAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* * * * * *
14167 CACCATAATGATTACAATTAGGCAATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
* * * * *
14232 AGACGATTCAAAATGGATCTAATGGGTCCTGATAGGTCCAAAATAACAAGTGTTCCAAATGAGCT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
*
14297 AAAAACTTCACAGTGGACTAATGTCACCAAAATGATTATAGTTAGGCCATACA-CAATGGAAAGA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA-ATCAATGGAAAGA
* *
14361 AAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGAAACTAATG
260 AAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * *
14410 AG-CCCGATAGGCCTAAAATAATAAGTGTTCCAAATGAGTT-AAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
14473 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
* * * ** * *
14538 AGACTATTCAATACGTAACTAATGGGCTTCGATAGGCCC-AAATAACGAGTATTCC-AATGAGCT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
*
14601 -AAAACTTCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCATAA-AAATGGAAAGAA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
* *
14663 AAGCATTGAGGTTTGCCAAACCGAAGACGATTCAAAACGGAACTAATG
261 AAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * ** * *
14711 GGCGCCGATAGGCCCAAAATAACAGGTGTTCCACGTGA-TCTATAAAGTTCACAGTGGACTAATC
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGT-TAAAAACTTCACAGTGGACTAATC
* *
14775 TCACCAAAATCATTATAGTTTGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
65 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
* * * * *
14840 AAGACGATTCAAAACGGAACTAATGAGCCCTGAAAGGCCCAAAATAACAAGTCTTCCAAATGAGT
130 AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* *
14905 TAAAAACTTCACAGTGGACTAATCTCACCCAAATGATTATAGTTAGGCCATAAACAATGGAAAG-
195 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGA
* ** * *
14969 AAAGCATCGAGGGATGCCAAATCAAAGACGATTCAAAACGGAACTAATG
260 AAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * * *
15018 GGCCCCGAAAGACCCAAAATAACAAGTGTTTCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* * * * *
15083 TACTAAAATGATTATAATTAGGTCATAAACAATGGAAA-AAAAGCATTGAGGTTTCCCAAAT---
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
* * *
15144 ---C-A---AAAACGGAACTAATGGGCCCCGTTAGGCCCAAGATAATAAGTGTTCCAAATGAGCT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* * * * * *
15202 TAAAACTTCAAAGTGGACTAATCTCACCATAATGATTACAATTAGGCAAT-ATCAATGGAAAGAA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
* * * *
15266 AAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACGGATCTAATG
261 AAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * * * * * *
15314 GGTCCTGATAGGTCCAAAATAACAAGTCTTCCAAATGAGCTAAAAACTTTACAGTGGACTAATGT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* * *
15379 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGTTTCCCAAACCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
* * * * *
15444 AGACTATTTAAAACGGAACTAATGAG-CCCGATAGGCCTAAAATAATAAGTGTTCCAAATGAGCT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* *
15508 AAAAACTTCACAGTGGACTAATCACACCAAAATGATTATAGTTAGGCCATAATCAATGGAATGAA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
* * * * **
15573 AAGCATTGAGCTTTCCCAAATCGAAAACGATTCAAAATGTCACTAATG
261 AAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * * *
15621 GGCTCCGATAGGCCCAAAGTAACAAGTGTACCAAATGAGTTAAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* * * * * *
15686 CACCATAATGATTACAGTTAGGCAATAAACAATGGAAGGAAAAGAATTGAGGTTTGCCAAGTCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
**
15751 AGACGATTCAAAACGGAACTTGTGGG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
15815 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
* *** *
15880 AAGCATTGA-GTTTGCCAAATCGAAGACGATTCAAAACTTCACTAAAG
261 AAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * *
15927 GG-CCCGATAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAGCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* *
15991 CACCAAAATTATTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGGTTT-CCTAAATCG
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC-AAATCG
* *
16055 AAGACGATTCAAAACGGAACTAATGGGCCCCGATATGCCTAAAATAACAAGTGTTCCAAATGAGC
130 AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* * * *
16120 TAAAAACTTCACAGTGGACTAATGTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAAA
195 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGA
* *
16185 AAAGAATTG-GTGTTTTCTAAATCGAAGACGATTCAAAACGGAACTAATG
260 AAAGCATTGAG-GTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * *
16234 GGCCCCGAAAGACCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* * * *
16299 CACCATAATGATTATAGTTAGGCCATAATCAATGGAAAGAAAAGAATTGAAGTTTGCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
*** * * * *
16364 AGACGATTCAAAACTTCACTAATGGG-CCCGTTAGGCCAAAAATAACAAATGTTCCAAATGAGTT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* *
16428 AAAAACTTCACAGTGGACTAACCTCACCAAAATTATTATAGTTAGGCCATAATCAATGGAAAGAA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
16493 AAGCATAT-AGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
261 AAGCAT-TGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* ** * *
16541 GGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAATTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
** * * * * *
16606 CACCGTAATGATTACAATTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTACCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
* * ** **
16671 AGACGATTCAAAATGGATCTAATGGGCCCTAATAGTTCCAAAATAACAAGTGTTCCAAATGAGCT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
*
16736 AAAAACTTCATAGTGG---------A-C----------TAGTTAGGCCATACA-CAATGGAAAGA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA-ATCAATGGAAAGA
*
16780 AAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGGAACTAATG
260 AAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * *
16829 GG-CCCGATAGGCCTAAAATAACAAGTGTTCCAAATAAGTTAAAAACTTCACAATGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* * * *
16893 CACCAAAATGATTATAGTTAGACCATAATCAATGGAAAGAAAAGCATTGAGCTTTCCCAAATCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
* ** * * * * *
16958 AGACGATTCAAAATGTCACTAATGAGCTCCGATAGGCCCAAAGTAACAAGTGTTCAAAATGAGTT
131 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* *
17023 AAAAACTTCTCAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAT-AATGGAAGGA
196 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT-AATCAATGGAAAGA
* * * * **
17087 AAAGAATTGAGGGTTGT-CAAGTCGAAGACGATTCAAAATGTCACTAATG
260 AAAGCATTGA-GGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * * *
17136 GGCTCCGATAGGCCCAAAGTAACAAGTGTACCAAATGAGTTAAAAACTTCAAAGTGGACTAATCT
1 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
* * * * * *
17201 CACCATAATGATTACAGTTAGGCAATAAACAATGGAAGGAAAAGAATTGAGGTTTGCCAAGTCGA
66 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
17266 AGACGATTCAAAACGG
131 AGACGATTCAAAACGG
17282 GTAATAACTT
Statistics
Matches: 3596, Mismatches: 428, Indels: 146
0.86 0.10 0.04
Matches are distributed among these distances:
287 177 0.05
288 72 0.02
289 1 0.00
295 11 0.00
296 227 0.06
297 22 0.01
298 1 0.00
299 2 0.00
300 1 0.00
301 59 0.02
302 167 0.05
303 142 0.04
304 25 0.01
305 162 0.05
306 688 0.19
307 1306 0.36
308 525 0.15
309 8 0.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (308 bp):
GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT
CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGA
AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAA
AAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATG
Found at i:18635 original size:307 final size:308
Alignment explanation
Indices: 17328--19940 Score: 3773
Period size: 307 Copynumber: 8.5 Consensus size: 308
17318 AGTTATACGA
17328 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
* * * * *
17393 AAGACGATTCAAAAC-GTCACTAATGGGCCCCGAAAGGACCAAAATAATAAGTGTTCCAAATGAT
66 AAGACGATTCAAAACAG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
** ** *
17457 CTAAAAACTTCACAAAGCCCTAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
130 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * * * *
17522 AAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGAAAGG-CA
195 AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* * * *
17586 AAAATAACAAGTGTTCCAAATGAGCTTAAAACATCAAAGTCGACTAATC
260 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
17635 TCACCAAAATGATTATAGTTAGGCCATAAACAGTGGAAAGAAAAGCATTGAGGTTTGCCAAATCA
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
* * * * * * * * *
17700 AAGATGATTCAAAACAAAACAAAAGGACCCCAATAGGTCCAAAATAAAAAGTGTTTCAAATGAGC
66 AAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
17765 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
131 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* * ** *
17830 AAGGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCTGATAGGCCCA
196 AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCA
* *
17895 AAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATG
261 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * * *
17943 TCACCAAAATGGTTATAGTTAGGCCATACACAATGGAAAGAAAAGCATTGAGGTTTGGCAAATTG
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
* * *
18008 AAGACGATTCAAAACATAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTCCCAAATGAGC
66 AAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
18073 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAACAATTGA
131 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT----AAACAA-TG-
* * * * *
18138 AAAAAAAAAGCATTG-GGGTTTACCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGAA
190 GAAAGAAAAGCATTGAGGG-TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
* *
18202 ATGCCCAAAATAACAAGTGTTCCAAATGAGCTACAAACTTCACAGTGGACTAATC
254 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * * *
18257 TCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAAAAAAGAATTG-GTGTTTTCCAAATC
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-GTTTGCCAAATC
* *
18321 GAAGACGATTCAAAACAGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTCTTCCAAATGAG
65 GAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
* * *
18386 TTAAAAACTTCACAGTGGACTAATCTCACCCAAATGATTATAGTTAGGCCATAAACATTGGAAAG
130 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * * * *
18451 -AAAGCATCGAGGGATGCCAAATCAAAGACAATTCAAAACGGAACTAATGGGCCCCGAAAGGCCC
195 AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* **
18515 AAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTTTACTAATC
260 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * * * * *
18564 TTACTAAAATGATTATAATTAAGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCA
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
** * *
18629 AAGACGATTCAAAATGGAACTAATGGGCCCCGGTAGGCCCAAGATAACAAGTGTTCCAAATGAGC
66 AAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* *
18694 TTAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
131 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* * * * *
18759 AAAGCATCGAGGGCTT-CCAAATCGAAGACAATTCAAAACGGATCTAATGGG-CCCGATAGTCCA
196 AAAGCATTGAGGG-TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* *
18822 AAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAAAC
260 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* ** * *
18871 TCACCAAACTTCTTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCG
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
* *
18936 AAGACGATTCAAAACGGAACTAATGGG-CCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGC
66 AAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* * *
19000 TACAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAATCAATGGAAAGA
131 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* *
19065 AAAGCATTGA-GGTTTCCAAAATCGAAAACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
196 AAAGCATTGAGGGTTGCC-AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
*
19129 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATC
260 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
19178 TCACCAAAATGATTATAGTTAGGCCATAATCAATGGAAAGAAAAGCATTAAGGTTT-CTAAAATC
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC-CAAATC
* *
19242 -AAGACGATTCAAAACGGAACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAG
65 GAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
* * * ** *
19306 TTAAAAACTTCACAGTGGACTAAGCTCACCAAACTTCTTATAGTTAGGCCATAATCAATGGAAAG
130 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * *
19371 AAAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATATGCCC
195 AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
*
19436 AAAATAACAAGTGTTCCAAATGAGCTACAAACTTCACAGTGGACTAATC
260 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
19485 TCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAA-AAAAGCATTG-GTGTTTTCCAAATC
1 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-GTTTGCCAAATC
*
19548 GAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGACCCAAAATAACAAGTGTTCCAAATGAG
65 GAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
* *
19613 CTAAAAACTTCAAAGTGGACTAATCTCACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
130 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * *
19678 AAAAGCATT-AGTGTTTCCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAGGCC
195 AAAAGCATTGAG-GGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* * *
19742 TAAAATAACAAGTGTTCCAAATGATCTAAAAACTTCAAAGTGGACTAATC
259 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
19792 TCACCATAATGATTACT-GTTAGGCCATAAACAATGGAAAGAAAA-CATCGAGGGTTGCCAAATC
1 TCACCAAAATGATTA-TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATC
* * * * *
19855 GAAGACGATTCAAAACAGATCTAATGGGCCCTGATAGGTCCAAAATAACAAGTGTTTCAATTGAG
65 GAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
19920 CTAAAAACTTCACAGTGGACT
130 CTAAAAACTTCACAGTGGACT
19941 GTAGACACTA
Statistics
Matches: 2081, Mismatches: 198, Indels: 54
0.89 0.08 0.02
Matches are distributed among these distances:
304 2 0.00
305 5 0.00
306 181 0.09
307 1333 0.64
308 273 0.13
309 3 0.00
310 5 0.00
312 6 0.00
313 5 0.00
314 268 0.13
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (308 bp):
TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
AAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCA
AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
Found at i:21272 original size:4 final size:4
Alignment explanation
Indices: 21243--21490 Score: 90
Period size: 4 Copynumber: 63.0 Consensus size: 4
21233 AAACCAAAAA
* * *
21243 TATT TTTT TA-T TATT TATT CA-C TATT TATTT TATT TATT TATT T-TT
1 TATT TATT TATT TATT TATT TATT TATT TA-TT TATT TATT TATT TATT
* * * * * * *
21289 AACTAT CATC TATT TATT TA-C TATT TATC AATT TATT TATT T-TT AACTAT
1 TA-T-T TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TA-T-T
* * * * *
21339 TATC TATT TATT TA-C TATT TATC TATT TATT TATT T-TT AACTAT TATC
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TA-T-T TATT
* * * * *
21387 AATT TATT TA-C TATT TATCT T-TT TATT TATT AATT TAAT TA-T TATC
1 TATT TATT TATT TATT TAT-T TATT TATT TATT TATT TATT TATT TATT
* * * ** *
21433 TATT TATT TA-C TATT TATCT T-CT TATT TATT AATT TAGC TA-T TATC
1 TATT TATT TATT TATT TAT-T TATT TATT TATT TATT TATT TATT TATT
21479 TATT TATT TATT
1 TATT TATT TATT
21491 ATTATTATCT
Statistics
Matches: 173, Mismatches: 49, Indels: 44
0.65 0.18 0.17
Matches are distributed among these distances:
3 27 0.16
4 126 0.73
5 14 0.08
6 6 0.03
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.64
Consensus pattern (4 bp):
TATT
Found at i:21293 original size:27 final size:26
Alignment explanation
Indices: 21243--21383 Score: 79
Period size: 27 Copynumber: 5.0 Consensus size: 26
21233 AAACCAAAAA
*
21243 TATTTTTTTATTATTTATTCACTATT
1 TATTTTTTTATTATTTATTAACTATT
21269 TATTTTATTTATTTATTT-TTAACTATCAT
1 TATTTT-TTTA-TTATTTATTAACTAT--T
* * * *
21298 CTATTTATTTACTATTTATCAATTTATT
1 -TATTTTTTTATTATTTATTAA-CTATT
*
21326 TATTTTTAACTATTATCTATTTATTTACTATT
1 TA-TTTT---T-TTAT-TATTTATTAACTATT
* *
21358 TATCTATTTATTTATTT-TTAACTATT
1 TATTTTTTTA-TTATTTATTAACTATT
21384 ATCAATTTAT
Statistics
Matches: 88, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
26 14 0.16
27 21 0.24
28 17 0.19
29 8 0.09
30 8 0.09
31 3 0.03
32 9 0.10
33 8 0.09
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.65
Consensus pattern (26 bp):
TATTTTTTTATTATTTATTAACTATT
Found at i:21333 original size:29 final size:25
Alignment explanation
Indices: 21299--21396 Score: 102
Period size: 25 Copynumber: 4.1 Consensus size: 25
21289 AACTATCATC
*
21299 TATTTATTTACTATTTATCAATTTATT
1 TATTT-TTAACTA-TTATCAATTTATT
21326 TATTTTTAACTATTATC----TATT
1 TATTTTTAACTATTATCAATTTATT
*
21347 TA--TTT-ACTATTTATCTATTTATT
1 TATTTTTAACTA-TTATCAATTTATT
21370 TATTTTTAACTATTATCAATTTATT
1 TATTTTTAACTATTATCAATTTATT
21395 TA
1 TA
21397 CTATTTATCT
Statistics
Matches: 61, Mismatches: 2, Indels: 18
0.75 0.02 0.22
Matches are distributed among these distances:
18 4 0.07
19 8 0.13
21 6 0.10
23 6 0.10
25 22 0.36
26 10 0.16
27 5 0.08
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTTTAACTATTATCAATTTATT
Found at i:21335 original size:44 final size:44
Alignment explanation
Indices: 21250--21493 Score: 339
Period size: 44 Copynumber: 5.5 Consensus size: 44
21240 AAATATTTTT
* *
21250 TTAT-TATTTATTCACTATTTATTTTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTA-TCTATTTATTTATTTTTAACTA
* *
21294 TCATCTATTTATTTACTATTTATCAATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
21338 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
* * *
21382 TTATCAATTTATTTACTATTTATCTTTTTATTTATTAATTTAATTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATT--TTTAACTA
*
21428 TTATCTATTTATTTACTATTTATCT-TCTTATTTATTAATTTAGCTA
1 TTATCTATTTATTTACTATTTATCTAT-TTATTTATT--TTTAACTA
*
21474 TTATCTATTTATTTATTATT
1 TTATCTATTTATTTACTATT
21494 ATTATCTTTT
Statistics
Matches: 183, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
44 99 0.54
45 17 0.09
46 67 0.37
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
Found at i:21422 original size:27 final size:26
Alignment explanation
Indices: 21392--21491 Score: 88
Period size: 27 Copynumber: 4.0 Consensus size: 26
21382 TTATCAATTT
21392 ATTTACTATTTATCTTTTTATTTATTA
1 ATTTACTA-TTATCTTTTTATTTATTA
* *
21419 ATTTA--ATTA-----TTATCTATTT
1 ATTTACTATTATCTTTTTATTTATTA
*
21438 ATTTACTATTTATCTTCTTATTTATTA
1 ATTTACTA-TTATCTTTTTATTTATTA
*
21465 ATTTAGCTATTATCTATTTATTTATTA
1 ATTTA-CTATTATCTTTTTATTTATTA
21492 TTATTATCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
19 13 0.22
21 1 0.02
22 3 0.05
24 3 0.05
25 1 0.02
27 34 0.59
28 3 0.05
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (26 bp):
ATTTACTATTATCTTTTTATTTATTA
Found at i:21450 original size:19 final size:19
Alignment explanation
Indices: 21264--21475 Score: 110
Period size: 19 Copynumber: 11.3 Consensus size: 19
21254 TATTTATTCA
21264 CTATTTATTT--TATTTAT
1 CTATTTATTTACTATTTAT
* * *
21281 TTATTT-TTAACTA-TCAT
1 CTATTTATTTACTATTTAT
21298 CTATTTATTTACTATTTAT
1 CTATTTATTTACTATTTAT
21317 CAATTTATTTATTTTTAACTA-TTAT
1 C----TATTTA--TTT-ACTATTTAT
21342 CTATTTATTTACTATTTAT
1 CTATTTATTTACTATTTAT
* *
21361 CTATTTATTTA-TTTTTAA
1 CTATTTATTTACTATTTAT
*
21379 CTATTATCAATT--TATTTA-
1 CTATT-T-ATTTACTATTTAT
*
21397 CTATTTA--T-CTTTTTAT
1 CTATTTATTTACTATTTAT
* * *
21413 TTATTAATTTAAT-TATTAT
1 CTATTTATTTACTAT-TTAT
21432 CTATTTATTTACTATTTAT
1 CTATTTATTTACTATTTAT
* *
21451 CT-TCTTATTTATTAATTTAG
1 CTAT-TTATTTACT-ATTTAT
21471 CTATT
1 CTATT
21476 ATCTATTTAT
Statistics
Matches: 152, Mismatches: 19, Indels: 45
0.70 0.09 0.21
Matches are distributed among these distances:
14 1 0.01
15 5 0.03
16 8 0.05
17 14 0.09
18 30 0.20
19 57 0.38
20 12 0.08
21 7 0.05
23 6 0.04
25 8 0.05
26 4 0.03
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (19 bp):
CTATTTATTTACTATTTAT
Done.