Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold561
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: 49595
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:1413 original size:28 final size:28
Alignment explanation
Indices: 1382--4448 Score: 2547
Period size: 28 Copynumber: 108.7 Consensus size: 28
1372 TTTAAAGTTT
* *
1382 ACAACTCAGTGGCACTCTTTTAAAGTCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
* * * * *
1410 ACAACTCCGTGGCACCCTTGT-AAGTCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
* * *
1437 ACAAATTC-GTGGCACCCTTTT-AAGTCC
1 AC-AAGTCAGTGGCACTCTTTTAAAGCCC
* * * * *
1464 ACAACTCTGTGGCACCCTTGT-AAGTCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
* * *
1491 ACAAATTC-GTGGCACCCTTTT-AAGTCC
1 AC-AAGTCAGTGGCACTCTTTTAAAGCCC
* * * *
1518 ACAACTCTGTGGCACCCTTTT-AAGTCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
* * * *
1545 ACAACTCTGTGGCACCCTTTT-AAGTCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
** * *
1572 ACAACTTTGTGGTGTGGCAC-CATTTAAAGTCC
1 ACAA----GT-CAGTGGCACTCTTTTAAAGCCC
* * * * *
1604 ATAACTCCGTGGCACCCTTTT-AAGTCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
* ** *
1631 ACAACTCTTTGGCACTCTTTTAAAGTCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
* * * * *
1659 ACCACTCTGTGGCACCCTTTT-AAGTCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
** * *
1686 ACAACACTGTGGCA-TCCTTTTAAAGTCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* * * ** *
1714 ATAACTCCGTGGCAC-CTTTTTTAGTCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
* *
1741 ACAACTTC-GTGGCACTCTTTTAAAGTCC
1 ACAA-GTCAGTGGCACTCTTTTAAAGCCC
** *
1769 ACAACACAGTGGCA-TCCTTTT-AAGTCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* * *
1796 ACAACTCTGTGGCA-TCTTTTTAAGTCCAC
1 ACAAGTCAGTGGCACTCTTTTAAAG-CC-C
* * *
1825 ACAACTCCGTGGCA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* * *
1853 ATAACTCAGTGGCACTCTTTTCAAAGCCT
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* * *
1882 GCAAGTCAGTGGCACCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
*
1910 ACAAGTCAGTGGCACTCTTTTCAAAGCCT
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
*
1939 ACAAGTCAGTGGCA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* *
1967 ACGAGTCAGTGGCACT-TTTTCATAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
*
1995 ACAAGTCAGTGGCACTTTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
*
2024 ACAAGTCAGTGGCACTCTTTTCAAAGCCA
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
2053 ACAAGTTAGTGGCAACT-TTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
* * * *
2081 ATAACTCAGTGGCACTATTTTCAAAGCCT
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* * *
2110 GCAAGTCAGTGGCACCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
*
2138 ACAAGTCAGTGGCACTCTTTTCAAAGCCT
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
*
2167 ACAAGTCAGTGGCA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* *
2195 ACGAGTCAGTGGCACT-TTTTCATAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
*
2223 ACAAGTCAGTGGCACTTTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
2252 ACAAGTCAGTGGCACTTTTTTCAAAGCCA
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
2281 ACAAGTTAGTGGCAACT-TTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
* * *
2309 ACAAATCAGTGGCACTATTTTCAAAGCCT
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
2338 ACAAGTCAGTGGCA-TCCTTTCAAAACCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* *
2366 ACGAGTCAGTGGCACTTTTTTCATAA-CCC
1 ACAAGTCAGTGGCACTCTTTT-A-AAGCCC
*
2395 ACAAGTCAGTGGCACTCTTTTCAAAGCCA
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
2424 ACAAGTTAGTGGCAACT-TTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
* *
2452 ACAAATCAGTGGCA-TCTTTTCAAAGCCT
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
*
2480 ACAAGTCAGTGGCACTTTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
2509 ACAAGTCAGTGGCA-TCCTCTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
2537 ACAAGTCAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
2566 ACAAGTTAGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
*
2594 ACAAATCAGTGGCA-TCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
2622 ACAAGTCAGTGGTACTTTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
2651 ACAAGTCAGTGGCA-TCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
2679 ACAAGTCAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
2708 ACAAGTCAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
2737 ACAAGTTAGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
* *
2765 ACAAGTTAGTGGCA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* *
2793 ACAAGTCAGTGGCA-TCCTTTCAAAGCTC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
*
2821 ACAAGTCAGTGGCATTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* * *
2850 ATAAGTTAGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
2878 ACATA-TCAGTGGCA-TCCTTTTAAAGCCC
1 ACA-AGTCAGTGGCACT-CTTTTAAAGCCC
* * * *
2906 ACGAGTCGGTGGCAAC-GTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
*
2934 TCAAGTCAG-GGACAAC-CTTTTAAAGCCC
1 ACAAGTCAGTGG-C-ACTCTTTTAAAGCCC
* * *
2962 ACGAGTTAGTGGCA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
*
2990 ACAAGGT-AGTGGCAAC-CTTTCAAAGCCC
1 ACAA-GTCAGTGGC-ACTCTTTTAAAGCCC
* *
3018 ACAAATCAGTGACA-TCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* ** *
3046 ACGAGTTGGTGGCAACT-TTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
* *
3074 AAAAGTTAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
3103 ACAAGTTAGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
*
3131 ACAAATCAGTGGCA-TCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* *
3159 ACGAGTCAGTGGCAGC-CTTTCAAAGCCC
1 ACAAGTCAGTGGCA-CTCTTTTAAAGCCC
* *
3187 ACAAGTTAGTGTCAC-CTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
*
3215 AAAAGAT-AGTGGCACTCTTTTCAAAGCCC
1 ACAAG-TCAGTGGCACTCTTTT-AAAGCCC
* *
3244 ACAAGTCAGTGGCACCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
3272 ACAAGTCAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
*
3301 ACAAATCAGTGGCA-TCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* * *
3329 ACGAGTCGGTGGCAACT-TTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
*
3357 ACAAGTCAGTTGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
3386 ACAAGTTAGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
* * * *
3414 ACAAATCAATAGCA-TCCTATTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
*
3442 ACAAGTTAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* * *
3471 ATAAGTTAGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
*
3499 ACAAATCAGTGGCA-TCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
3527 ACAAGTCAGTTGCA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
*
3555 ACAAGTCAGTGGCA-TCATTTCAAAGCCC
1 ACAAGTCAGTGGCACTC-TTTTAAAGCCC
3583 ACAAGTCAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* * *
3612 ATAAGTTAGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
*
3640 ACAAATCAGTGGCA-TCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* * *
3668 ACGAGTCGGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
** *
3696 TGAAGTCAGTGGCA-TCCTTCTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
*
3724 ACAAGTCAGTGGCA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* *
3752 ACAAGGT-AGTGGCAAC-CTTTCAAAGTCC
1 ACAA-GTCAGTGGC-ACTCTTTTAAAGCCC
*
3780 ACAAATCAGTGGCA-TCATTTTAAAGCCC
1 ACAAGTCAGTGGCACTC-TTTTAAAGCCC
* *
3808 ACGAGTCAGTGGCAGC-CTTTCAAAGCCC
1 ACAAGTCAGTGGCA-CTCTTTTAAAGCCC
**
3836 ACAAGTCAGTGTTAC-CTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
3864 ATAAGACAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
3893 ACAAGTCAGTGGCACCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
*
3921 ACAAGTCAATGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
3950 ACAAAATCAGTGCCA-TCCTTTTAAAGCCC
1 AC-AAGTCAGTGGCACT-CTTTTAAAGCCC
* *
3979 ACGAGTCAGTGGCAACT-TTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
4007 ACAAGTCAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
4036 ACAAGTTAGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
*
4064 ACAAATCAGTGGCA-TCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
*
4092 ACAAGTCAGTGGCA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* * *
4120 ATAAGTTAGTGGCAAC-CTTTCAAAGCCC
1 ACAAGTCAGTGGC-ACTCTTTTAAAGCCC
*
4148 ACAAATCAGTGGCA-TCTTTTTAAAGCCC
1 ACAAGTCAGTGGCACTC-TTTTAAAGCCC
** * * *
4176 ATGAGTCGGTGGAAACT-TTTCAAAGCCC
1 ACAAGTCAGTGG-CACTCTTTTAAAGCCC
* *
4204 ACAAATCACTGGCA-TCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* * *
4232 ACGAGTCAGTGGTA-TCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
*
4260 ACAAATCAGTGGCA-TCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* * *
4288 ACGAGTCAGTGGCACCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTTAAAGCCC
*
4316 ACAAGTCTGTGGCA-TCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACT-CTTTTAAAGCCC
* * * *
4344 ACGAGTCAGTGGTAGC-CTTTCAAAGCTC
1 ACAAGTCAGTGGCA-CTCTTTTAAAGCCC
*
4372 ACAAGTCAGTGTCAC-CTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
* *
4400 ATAAGACAGTGGCACTCTTTTCAAAGCCC
1 ACAAGTCAGTGGCACTCTTTT-AAAGCCC
4429 ACAAGTCAGTGGCACTCTTT
1 ACAAGTCAGTGGCACTCTTT
4449 CACATCCGCC
Statistics
Matches: 2544, Mismatches: 341, Indels: 307
0.80 0.11 0.10
Matches are distributed among these distances:
26 15 0.01
27 285 0.11
28 1459 0.57
29 712 0.28
30 51 0.02
31 5 0.00
32 17 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
ACAAGTCAGTGGCACTCTTTTAAAGCCC
Found at i:1447 original size:27 final size:27
Alignment explanation
Indices: 1390--1844 Score: 352
Period size: 27 Copynumber: 16.4 Consensus size: 27
1380 TTACAACTCA
* * *
1390 GTGGCACTCTTTTAAAGTCCACAACTCC
1 GTGGCACCCTTTT-AAGTCCACAAATTC
*
1418 GTGGCACCCTTGTAAGTCCACAAATTC
1 GTGGCACCCTTTTAAGTCCACAAATTC
*
1445 GTGGCACCCTTTTAAGTCCAC-AACTC
1 GTGGCACCCTTTTAAGTCCACAAATTC
*
1471 TGTGGCACCCTTGTAAGTCCACAAATTC
1 -GTGGCACCCTTTTAAGTCCACAAATTC
*
1499 GTGGCACCCTTTTAAGTCCAC-AACTC
1 GTGGCACCCTTTTAAGTCCACAAATTC
*
1525 TGTGGCACCCTTTTAAGTCCAC-AACTC
1 -GTGGCACCCTTTTAAGTCCACAAATTC
* *
1552 TGTGGCACCCTTTTAAGTCCACAACTTTGTGGT
1 -GTGGCACCCTTTTAAGTCCACAA--AT-T--C
* * * * *
1585 GTGGCACCATTTAAAGTCCATAACTCC
1 GTGGCACCCTTTTAAGTCCACAAATTC
*
1612 GTGGCACCCTTTTAAGTCCAC-AACTC
1 GTGGCACCCTTTTAAGTCCACAAATTC
* * * *
1638 TTTGGCACTCTTTTAAAGTCCAC-CACTC
1 -GTGGCACCCTTTT-AAGTCCACAAATTC
*
1666 TGTGGCACCCTTTTAAGTCCACAACACT-
1 -GTGGCACCCTTTTAAGTCCACAA-ATTC
* * * *
1694 GTGGCATCCTTTTAAAGTCCATAACTCC
1 GTGGCACCCTTTT-AAGTCCACAAATTC
* * *
1722 GTGGCACCTTTTTTAGTCCACAACTTC
1 GTGGCACCCTTTTAAGTCCACAAATTC
*
1749 GTGGCACTCTTTTAAAGTCCACAACA--C
1 GTGGCACCCTTTT-AAGTCCACAA-ATTC
* *
1776 AGTGGCATCCTTTTAAGTCCAC-AACTC
1 -GTGGCACCCTTTTAAGTCCACAAATTC
* * *
1803 TGTGGCATCTTTTTAAGTCCACACAACTCC
1 -GTGGCACCCTTTTAAGTCCACA-AA-TTC
*
1833 GTGGCATCCTTT
1 GTGGCACCCTTT
1845 CAAAGCCCAT
Statistics
Matches: 352, Mismatches: 52, Indels: 45
0.78 0.12 0.10
Matches are distributed among these distances:
25 1 0.00
26 11 0.03
27 221 0.63
28 80 0.23
29 16 0.05
30 2 0.01
31 1 0.00
32 20 0.06
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (27 bp):
GTGGCACCCTTTTAAGTCCACAAATTC
Found at i:1476 original size:54 final size:55
Alignment explanation
Indices: 1390--1935 Score: 486
Period size: 55 Copynumber: 9.8 Consensus size: 55
1380 TTACAACTCA
* * *
1390 GTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTGT-AAGTCCACAAATTC
1 GTGGCACCCTTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAAATTC
*
1445 GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTGT-AAGTCCACAAATTC
1 GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAAATTC
*
1499 GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTT-AAGTCCAC-AACTC
1 GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAAATTC
* * * * *
1552 TGTGGCACCCTTTTAAGTCCACAACTTTGTGGTGTGGCA-CCATTTAAAGTCCATAACTCC
1 -GTGGCACCCTTTTAAGTCCACAAC----T-CTGTGGCACCCTTTTAAAGTCCACAAATTC
* * * *
1612 GTGGCACCCTTTTAAGTCCACAACTCTTTGGCACTCTTTTAAAGTCCAC-CACTC
1 GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAAATTC
* * * * *
1666 TGTGGCACCCTTTTAAGTCCACAACACTGTGGCATCCTTTTAAAGTCCATAACTCC
1 -GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAAATTC
* * *
1722 GTGGCACCTTTTTTAGTCCACAACT-TCGTGGCACTCTTTTAAAGTCCACAACA--C
1 GTGGCACCCTTTTAAGTCCACAACTCT-GTGGCACCCTTTTAAAGTCCACAA-ATTC
* * * *
1776 AGTGGCATCCTTTTAAGTCCACAACTCTGTGGCA-TCTTTTTAAGTCCACACAACTCC
1 -GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACA-AA-TTC
* * * * * * * *
1833 GTGGCATCCTTTCAAAGCCCATAACTCAGTGGCACTCTTTTCAAAG-CCTGC-AAGTC
1 GTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACCCTTTT-AAAGTCC-ACAAATTC
* * * * *
1889 AGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
1 -GTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACCCTTTT-AAAG
1936 CCTACAAGTC
Statistics
Matches: 417, Mismatches: 50, Indels: 46
0.81 0.10 0.09
Matches are distributed among these distances:
53 4 0.01
54 136 0.33
55 141 0.34
56 15 0.04
57 63 0.15
58 14 0.03
59 42 0.10
60 2 0.00
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (55 bp):
GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAAATTC
Found at i:1678 original size:55 final size:55
Alignment explanation
Indices: 1371--2740 Score: 579
Period size: 57 Copynumber: 24.3 Consensus size: 55
1361 TGGCATTTCT
** * * * *
1371 TTTTAAAGTTTACAACTCAGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCTGTGGCACCCTTTT-AAGTCCACAACTCTGTGGCACTC
* * *
1427 TTGT-AAGTCCACAAAT-TCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAAGTCCACAACTCT-GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACTC
* * *
1481 TTGT-AAGTCCACAAAT-TCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAAGTCCACAACTCT-GTGGCACCCTTTTAAGTCCACAACTCTGTGGCACTC
*
1535 TTTT-AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTTTGTGGTGTGGCAC-C
1 TTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAAC----T-CTGTGGCACTC
* * * *
1593 ATTTAAAGTCCATAACTCCGTGGCACCCTTTTAAGTCCACAACTCTTTGGCACTC
1 TTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACTC
* *
1648 TTTTAAAGTCCACCACTCTGTGGCACCCTTTTAAGTCCACAACACTGTGGCA-TCC
1 TTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACT-C
* * * *
1703 TTTTAAAGTCCATAACTCCGTGGCACCTTTTTTAGTCCACAACT-TCGTGGCACTC
1 TTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCT-GTGGCACTC
* * *
1758 TTTTAAAGTCCACAACACAGTGGCATCCTTTTAAGTCCACAACTCTGTGGCA-TC
1 TTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACTC
* * * * * * *
1812 TTTTTAAGTCCACACAACTCCGTGGCATCCTTTCAAAGCCCATAACTCAGTGGCACTC
1 TTTTAAAGT-C-CACAACTCTGTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACTC
* * * * * * *
1870 TTTTCAAAG-CCTGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTT-AAAGTCC-ACAACTCTGTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACTC
* * * * * * * *
1927 TTTTCAAAG-CCTACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCACT-
1 TTTT-AAAGTCC-ACAACTCTGTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACTC
* * * * ** * * *
1983 TTTTCATAGCCCACAAGTCAGTGGCACTTTTTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTT-AAAGTCCACAACTCTGTGGCACCCTTTT--AAGTCCACAACTCTGTGGCACTC
* * * * * *
2041 TTTTCAAAG-CCAACAAGT-TAGTGGCA-ACTTTTCAAAGCCCATAACTCAGTGGCACTA
1 TTTT-AAAGTCC-ACAACTCT-GTGGCACCCTTTT--AAGTCCACAACTCTGTGGCACTC
* * * * * * *
2098 TTTTCAAAG-CCTGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTT-AAAGTCC-ACAACTCTGTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACTC
* * * * * * * *
2155 TTTTCAAAG-CCTACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCACT-
1 TTTT-AAAGTCC-ACAACTCTGTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACTC
* * * * ** * * * *
2211 TTTTCATAGCCCACAAGTCAGTGGCACTTTTTTCAAAGCCCACAAGTCAGTGGCACTT
1 TTTT-AAAGTCCACAACTCTGTGGCACCCTTTT--AAGTCCACAACTCTGTGGCACTC
* * * * * *
2269 TTTTCAAAG-CCAACAAGT-TAGTGGCA-ACTTTTCAAAGCCCACAAATCAGTGGCACTA
1 TTTT-AAAGTCC-ACAACTCT-GTGGCACCCTTTT--AAGTCCACAACTCTGTGGCACTC
* * * * ** * * * *
2326 TTTTCAAAG-CCTACAAGTCAGTGGCATCCTTTCAAAACCCACGAGTCAGTGGCACTT
1 TTTT-AAAGTCC-ACAACTCTGTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACTC
* * * * *
2383 TTTTCATAA-CCCACAAGTCAGTGGCACTCTTTTCAAAG-CCAACAAGT-TAGTGGCAACT-
1 TTTT-A-AAGTCCACAACTCTGTGGCACCCTTTT--AAGTCC-ACAACTCT-GTGGC-ACTC
* * * * * * * *
2441 TTTCAAAGCCCACAAATCAGTGGCA-TCTTTTCAAAG-CCTACAAGTCAGTGGCACTT
1 TTTTAAAGTCCACAACTCTGTGGCACCCTTTT--AAGTCC-ACAACTCTGTGGCACTC
* * * * ** * * *
2497 TTTTCAAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTT-AAAGTCCACAACTCTGTGGCACCCT-TTTAAGTCCACAACTCTGTGGCACTC
* * * * * * *
2554 TTTTCAAAGCCCACAAGT-TAGTGGCAACCTTTCAAAGCCCACAAATCAGTGGCA-TC
1 TTTT-AAAGTCCACAACTCT-GTGGCACCCTTT-TAAGTCCACAACTCTGTGGCACTC
* * * * ** * * *
2610 TTTTCAAAGCCCACAAGTCAGTGGTACTTTTTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTT-AAAGTCCACAACTCTGTGGCACCCTTTT--AAGTCCACAACTCTGTGGCACT-C
* * * * * * *
2668 TTTTAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTTAAAGTCCACAACTCTGTGGCACCCTTTT--AAGTCCACAACTCTGTGGCACTC
*
2725 TTTTCAAAGCCCACAA
1 TTTT-AAAGTCCACAA
2741 GTTAGTGGCA
Statistics
Matches: 1132, Mismatches: 123, Indels: 116
0.83 0.09 0.08
Matches are distributed among these distances:
54 133 0.12
55 164 0.14
56 133 0.12
57 552 0.49
58 99 0.09
59 51 0.05
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (55 bp):
TTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACTC
Found at i:1894 original size:57 final size:57
Alignment explanation
Indices: 1749--4450 Score: 3099
Period size: 57 Copynumber: 47.8 Consensus size: 57
1739 CCACAACTTC
* ** * * * *
1749 GTGGCACTCTTTT-AAAGTCCACAACACAGTGGCATCCTTT-TAAGTCCACAACTCT
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * * *
1804 GTGGCA-TCTTTT-TAAGTCCACACAACTCCGTGGCATCCTTTCAAAGCCCATAACTCA
1 GTGGCACTCTTTTCAAAG-CC-CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
** *
1861 GTGGCACTCTTTTCAAAGCCTGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* *
1918 GTGGCACTCTTTTCAAAGCCTACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* **
1975 GTGGCACT-TTTTCATAGCCCACAAGTCAGTGGCACTTTTTTCAAAGCCCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCA
* * * * * *
2032 GTGGCACTCTTTTCAAAGCCAACAAGTTAGTGGCAACTTTTCAAAGCCCATAACTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* ** *
2089 GTGGCACTATTTTCAAAGCCTGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* *
2146 GTGGCACTCTTTTCAAAGCCTACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* **
2203 GTGGCACT-TTTTCATAGCCCACAAGTCAGTGGCACTTTTTTCAAAGCCCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCA
* * * * * *
2260 GTGGCACTTTTTTCAAAGCCAACAAGTTAGTGGCAACTTTTCAAAGCCCACAAATCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
2317 GTGGCACTATTTTCAAAGCCTACAAGTCAGTGGCATCCTTTCAAAACCCACGAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
2374 GTGGCACTTTTTTCATAA-CCCACAAGTCAGTGGCACTCTTTTCAAAGCCAACAAGTTA
1 GTGGCACTCTTTTCA-AAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCA
* * * *
2432 GTGGCA-ACTTTTCAAAGCCCACAAATCAGTGGCATCTTTTCAAAGCCTACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* *
2488 GTGGCACTTTTTTCAAAGCCCACAAGTCAGTGGCATCCTCTCAAAGCCCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * *
2545 GTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAATCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* **
2602 GTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGTACTTTTTTCAAAGCCCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCA
*
2659 GTGGCA-TCCTTTT-AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCA
1 GTGGCACT-CTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCA
* * *
2716 GTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAGTTA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* *
2773 GTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCTCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
2829 GTGGCATTCTTTTCAAAGCCCATAAGTTAGTGGCAACCTTTCAAAGCCCACATA-TCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACA-AGTCA
* * * * *
2886 GTGGCA-TCCTTTT-AAAGCCCACGAGTCGGTGGCAACGTTTCAAAGCCCTCAAGTCA
1 GTGGCACT-CTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* *
2942 G-GGACAAC-CTTTT-AAAGCCCACGAGTTAGTGGCATCCTTTCAAAGCCCACAAGGT-A
1 GTGG-C-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAA-GTCA
* * * * **
2998 GTGGCAAC-C-TTTCAAAGCCCACAAATCAGTGACATCCTTTTAAAGCCCACGAGTTG
1 GTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * * *
3054 GTGGCA-ACTTTTCAAAGCCCAAAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTTA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCA
* * *
3111 GTGGCAAC-C-TTTCAAAGCCCACAAATCAGTGGCATCCTTTTAAAGCCCACGAGTCA
1 GTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * *
3167 GTGGCAGC-C-TTTCAAAGCCCACAAGTTAGTGTCA-CCTTTTCAAAGCCCAAAAGAT-A
1 GTGGCA-CTCTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAG-TCA
*
3223 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
3280 GTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCATCCTTTTAAAGCCCACGAGTCG
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
3337 GTGGCA-ACTTTTCAAAGCCCACAAGTCAGTTGCACTCTTTTCAAAGCCCACAAGTTA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCA
* * * *
3394 GTGGCAAC-C-TTTCAAAGCCCACAAATCAATAGCATCCTATT-AAAGCCCACAAGTTA
1 GTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCT-TTCAAAGCCCACAAGTCA
* * * *
3450 GTGGCACTCTTTTCAAAGCCCATAAGTTAGTGGCAACCTTTCAAAGCCCACAAATCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
*
3507 GTGGCA-TCTTTTCAAAGCCCACAAGTCAGTTGCATCCTTTCAAAGCCCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
3563 GTGGCA-TCATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAGTTA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCA
* * * *
3620 GTGGCAAC-C-TTTCAAAGCCCACAAATCAGTGGCATCCTTTTAAAGCCCACGAGTCG
1 GTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
**
3676 GTGGCAAC-C-TTTCAAAGCCCTGAAGTCAGTGGCATCC-TTCTAAAGCCCACAAGTCA
1 GTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC-AAAGCCCACAAGTCA
* * * *
3732 GTGGCA-TCCTTTCAAAGCCCACAAGGT-AGTGGCAACCTTTCAAAGTCCACAAATCA
1 GTGGCACTCTTTTCAAAGCCCACAA-GTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* *
3788 GTGGCA-TCATTTT-AAAGCCCACGAGTCAGTGGCAGCCTTTCAAAGCCCACAAGTCA
1 GTGGCACTC-TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
** * * *
3844 GTGTTAC-CTTTTCAAAGCCCATAAGACAGTGGCACTCTTTTCAAAGCCCACAAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCA
* * * *
3901 GTGGCAC-CCTTTCAAAGCCCACAAGTCAATGGCACTCTTTTCAAAGCCCACAAAATCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCAC-AAGTCA
* * * *
3959 GTGCCA-TCCTTTT-AAAGCCCACGAGTCAGTGGCAACTTTTCAAAGCCCACAAGTCA
1 GTGGCACT-CTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * *
4015 GTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAACCTTTCAAAGCCCACAAATCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* *
4072 GTGGCA-TCCTTTT-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTTA
1 GTGGCACT-CTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * ** *
4128 GTGGCAAC-C-TTTCAAAGCCCACAAATCAGTGGCATCTTTTTAAAGCCCATGAGTCG
1 GTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
** * * * *
4184 GTGG-AAACTTTTCAAAGCCCACAAATCACTGGCATCCTTTTAAAGCCCACGAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * * *
4240 GTGGTA-TCCTTTCAAAGCCCACAAATCAGTGGCATCCTTTTAAAGCCCACGAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
4296 GTGGCAC-CCTTTCAAAGCCCACAAGTCTGTGGCATCCTTTTAAAGCCCACGAGTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * * * *
4352 GTGGTAGC-C-TTTCAAAGCTCACAAGTCAGTGTCA-CCTTTTCAAAGCCCATAAGACA
1 GTGGCA-CTCTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCA
4408 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCA
1 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCA
4451 CATCCGCCCA
Statistics
Matches: 2304, Mismatches: 265, Indels: 154
0.85 0.10 0.06
Matches are distributed among these distances:
54 10 0.00
55 40 0.02
56 977 0.42
57 1126 0.49
58 144 0.06
59 7 0.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (57 bp):
GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCA
Found at i:1974 original size:85 final size:85
Alignment explanation
Indices: 1694--4448 Score: 2994
Period size: 85 Copynumber: 32.5 Consensus size: 85
1684 CCACAACACT
* * * * * ** * *
1694 GTGGCATCCTTTTAAAGTCCATAACTCCGTGGCACCTTTT-TTAGTCCACAACTTC-GTGGCACT
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAA-GTCAGTGGCACT
* **
1757 CTTTT-AAAGTCCACAACACA
65 CTTTTCAAAGCCCACAAGTCA
* * * * * * * *
1777 GTGGCATCCTTT-TAAGTCCACAACTCTGTGGCATCTTTT-TAAGTCCACACAACTCCGTGGCA-
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG-CC-CACAAGTCAGTGGCAC
* * *
1839 TCCTTTCAAAGCCCATAACTCA
64 TCTTTTCAAAGCCCACAAGTCA
* ** *
1861 GTGGCACTCTTTTCAAAGCCTGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT
*
1926 CTTTTCAAAGCCTACAAGTCA
65 CTTTTCAAAGCCCACAAGTCA
* * * *
1947 GTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCACTTTTTCATAGCCCACAAGTCAGTGGCACTT
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTC
2012 TTTTCAAAGCCCACAAGTCA
66 TTTTCAAAGCCCACAAGTCA
* * * * * *
2032 GTGGCACTCTTTTCAAAGCCAACAAGTTAGTGGCAACTTTTCAAAGCCCATAACTCAGTGGCACT
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT
* **
2097 ATTTTCAAAGCCTGCAAGTCA
65 CTTTTCAAAGCCCACAAGTCA
* *
2118 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCTACAAGTCAGTGGCA-T
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
2182 CCTTTCAAAGCCCACGAGTCA
65 CTTTTCAAAGCCCACAAGTCA
* * *
2203 GTGGCA-CTTTTTCATAGCCCACAAGTCAGTGGCACTTTTTTCAAAGCCCACAAGTCAGTGGCAC
1 GTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
2267 TTTTTTCAAAGCCAACAAGTTA
64 TCTTTTCAAAGCCCACAAGTCA
* * * * *
2289 GTGGCAACTTTTCAAAGCCCACAAATCAGTGGCACTATTTTCAAAGCCTACAAGTCAGTGGCA-T
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
2353 CCTTTCAAAACCCACGAGTCA
65 CTTTTCAAAGCCCACAAGTCA
** * *
2374 GTGGCACTTTTTTCATAA-CCCACAAGTCAGTGGCACTCTTTTCAAAGCCAACAAGTTAGTGGCA
1 GTGGCA-TCCTTTCA-AAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCA
* *
2438 -ACTTTTCAAAGCCCACAAATCA
63 CTCTTTTCAAAGCCCACAAGTCA
* * *
2460 GTGGCATCTTTTCAAAGCCTACAAGTCAGTGGCACTTTTTTCAAAGCCCACAAGTCAGTGGCA-T
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
2524 CCTCTCAAAGCCCACAAGTCA
65 CTTTTCAAAGCCCACAAGTCA
* * *
2545 GTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAACC-TTTCAAAGCCCACAAATCAGTGGCA-
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGCAC
2608 TCTTTTCAAAGCCCACAAGTCA
64 TCTTTTCAAAGCCCACAAGTCA
* **
2630 GTGGTACTTTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTT-AAAGCCCACAAGTCAGTGGCAC
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCAC
2694 TCTTTTCAAAGCCCACAAGTCA
64 TCTTTTCAAAGCCCACAAGTCA
* * *
2716 GTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAACC-TTTCAAAGCCCACAAGTTAGTGGCA-
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGCAC
*
2779 TCCTTTCAAAGCCCACAAGTCA
64 TCTTTTCAAAGCCCACAAGTCA
* * * *
2801 GTGGCATCCTTTCAAAGCTCACAAGTCAGTGGCATTCTTTTCAAAGCCCATAAGTTAGTGGCAAC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGC-AC
2866 -C-TTTCAAAGCCCACATA-TCA
64 TCTTTTCAAAGCCCACA-AGTCA
* * * * * *
2886 GTGGCATCCTTTTAAAGCCCACGAGTCGGTGGCAACGTTTCAAAGCCCTCAAGTCAG-GGACAAC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGG-C-AC
* *
2950 -CTTTT-AAAGCCCACGAGTTA
64 TCTTTTCAAAGCCCACAAGTCA
* *
2970 GTGGCATCCTTTCAAAGCCCACAAGGT-AGTGGCAACC-TTTCAAAGCCCACAAATCAGTGACA-
1 GTGGCATCCTTTCAAAGCCCACAA-GTCAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGCAC
* **
3032 TCCTTTT-AAAGCCCACGAGTTG
64 T-CTTTTCAAAGCCCACAAGTCA
* * * * *
3054 GTGGCAACTTTTCAAAGCCCAAAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAAC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGC-AC
*
3119 -C-TTTCAAAGCCCACAAATCA
64 TCTTTTCAAAGCCCACAAGTCA
* * * *
3139 GTGGCATCCTTTTAAAGCCCACGAGTCAGTGGCAGCC-TTTCAAAGCCCACAAGTTAGTGTCAC-
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3202 CTTTTCAAAGCCCAAAAGAT-A
65 CTTTTCAAAGCCCACAAG-TCA
* *
3223 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3288 CTTTTCAAAGCCCACAAATCA
65 CTTTTCAAAGCCCACAAGTCA
* * * * *
3309 GTGGCATCCTTTTAAAGCCCACGAGTCGGTGGCAACTTTTCAAAGCCCACAAGTCAGTTGCACTC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTC
*
3374 TTTTCAAAGCCCACAAGTTA
66 TTTTCAAAGCCCACAAGTCA
* * * * * *
3394 GTGGCAACCTTTCAAAGCCCACAAATCAATAGCATCCTATT-AAAGCCCACAAGTTAGTGGCACT
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
3458 CTTTTCAAAGCCCATAAGTTA
65 CTTTTCAAAGCCCACAAGTCA
* * * *
3479 GTGGCAACCTTTCAAAGCCCACAAATCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTTGCA-TC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTC
*
3543 CTTTCAAAGCCCACAAGTCA
66 TTTTCAAAGCCCACAAGTCA
* * *
3563 GTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAGTTAGTGGCAAC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGC-AC
*
3628 -C-TTTCAAAGCCCACAAATCA
64 TCTTTTCAAAGCCCACAAGTCA
* * * **
3648 GTGGCATCCTTTTAAAGCCCACGAGTCGGTGGCAACC-TTTCAAAGCCCTGAAGTCAGTGGCA-T
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGCACT
*
3711 C-CTTCTAAAGCCCACAAGTCA
65 CTTTTC-AAAGCCCACAAGTCA
* *
3732 GTGGCATCCTTTCAAAGCCCACAAGGT-AGTGGCAACC-TTTCAAAGTCCACAAATCAGTGGCA-
1 GTGGCATCCTTTCAAAGCCCACAA-GTCAGTGGC-ACCTTTTCAAAGCCCACAAGTCAGTGGCAC
*
3794 TCATTTT-AAAGCCCACGAGTCA
64 TC-TTTTCAAAGCCCACAAGTCA
* ** * *
3816 GTGGCAGCCTTTCAAAGCCCACAAGTCAGTGTTACCTTTTCAAAGCCCATAAGACAGTGGCACTC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTC
3881 TTTTCAAAGCCCACAAGTCA
66 TTTTCAAAGCCCACAAGTCA
* * * *
3901 GTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACTCTTTTCAAAGCCCACAAAATCAGTGCCA-
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCAC-AAGTCAGTGGCAC
*
3965 TCCTTTT-AAAGCCCACGAGTCA
64 T-CTTTTCAAAGCCCACAAGTCA
* * *
3987 GTGGCAACTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAAC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGC-AC
*
4052 -C-TTTCAAAGCCCACAAATCA
64 TCTTTTCAAAGCCCACAAGTCA
* * *
4072 GTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCATAAGTTAGTGGCAAC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGC-AC
*
4136 -C-TTTCAAAGCCCACAAATCA
64 TCTTTTCAAAGCCCACAAGTCA
* * ** * * * * *
4156 GTGGCATCTTTTTAAAGCCCATGAGTCGGTGGAAACTTTTCAAAGCCCACAAATCACTGGCA-TC
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACT-
*
4220 CTTTT-AAAGCCCACGAGTCA
65 CTTTTCAAAGCCCACAAGTCA
* * *
4240 GTGGTATCCTTTCAAAGCCCACAAATCAGTGGCATCCTTTT-AAAGCCCACGAGTCAGTGGCAC-
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
4303 CCTTTCAAAGCCCACAAGTCT
65 CTTTTCAAAGCCCACAAGTCA
* * * * *
4324 GTGGCATCCTTTTAAAGCCCACGAGTCAGTGGTAGCC-TTTCAAAGCTCACAAGTCAGTGTCAC-
1 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
4387 CTTTTCAAAGCCCATAAGACA
65 CTTTTCAAAGCCCACAAGTCA
*
4408 GTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTT
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTT
4449 CACATCCGCC
Statistics
Matches: 2296, Mismatches: 294, Indels: 161
0.83 0.11 0.06
Matches are distributed among these distances:
82 26 0.01
83 51 0.02
84 686 0.30
85 1001 0.44
86 509 0.22
87 23 0.01
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (85 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTC
TTTTCAAAGCCCACAAGTCA
Found at i:4601 original size:21 final size:21
Alignment explanation
Indices: 4575--4652 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
4565 AAAATTATCC
4575 AAATGTATCGATACATTTGTA
1 AAATGTATCGATACATTTGTA
*
4596 AAATGTATCGATACATTTGTG
1 AAATGTATCGATACATTTGTA
* *
4617 GAATGTATCGATACA-TTCTA
1 AAATGTATCGATACATTTGTA
4637 CAAATGTATCGATACA
1 -AAATGTATCGATACA
4653 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (21 bp):
AAATGTATCGATACATTTGTA
Found at i:4768 original size:20 final size:20
Alignment explanation
Indices: 4743--4795 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4733 GCCAAGGGAA
***
4743 TGTATCGATACATTTTTCTG
1 TGTATCGATACATGGATCTG
*
4763 TGTATCGATACATGGATCTT
1 TGTATCGATACATGGATCTG
4783 TGTATCGATACAT
1 TGTATCGATACAT
4796 CTTGAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATGGATCTG
Found at i:7254 original size:52 final size:51
Alignment explanation
Indices: 7135--7267 Score: 176
Period size: 52 Copynumber: 2.6 Consensus size: 51
7125 TTGAGTTTCT
* * *
7135 CAATTCTCCACAATTTGGGATATTCCAACTCCGATTTTATTTTCAAAACAC
1 CAATTTTCCACAATTGGGGATATTCCAACTCCGATTTTATTTCCAAAACAC
** *
7186 CAATTTTCCTTTAATTGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTCC-ACAATTGGGGATATTCCAACTCCGATTTTATTTCC-AAAACAC
* *
7239 CAATTTTTCACAATTGAGGATATTCCAAC
1 CAATTTTCCACAATTGGGGATATTCCAAC
7268 CTCGTTATTT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 8 0.12
52 46 0.67
53 15 0.22
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (51 bp):
CAATTTTCCACAATTGGGGATATTCCAACTCCGATTTTATTTCCAAAACAC
Found at i:7427 original size:79 final size:79
Alignment explanation
Indices: 7283--7482 Score: 217
Period size: 79 Copynumber: 2.5 Consensus size: 79
7273 TATTTCATCG
** * *
7283 GGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCGGCTTTATTCCCAAAATATCG
1 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATCG
* *
7348 ATTTCTCATAAATA
66 ATTTCTCACAAACA
* * *
7362 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATG-TTT-TTCTC-TAATCA
1 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG--GCTTTATTCCCAAAAT-A
* *
7424 TCGATTTCTCACAACCG
63 TCGATTTCTCACAAACA
* * * *
7441 GGGATACTCCAGCCCCGTCATTTTCAAGGGGACACTCCAACC
1 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACC
7483 TCGTTATTAT
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
78 3 0.03
79 95 0.93
80 3 0.03
81 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.27
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATCG
ATTTCTCACAAACA
Found at i:13134 original size:13 final size:13
Alignment explanation
Indices: 13091--13117 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13081 CAATTCTTCA
13091 TGTATCGATACAT
1 TGTATCGATACAT
13104 TGTATCGATACAT
1 TGTATCGATACAT
13117 T
1 T
13118 ATACCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13925 original size:21 final size:22
Alignment explanation
Indices: 13884--13937 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
13874 CGTTGACCAT
13884 GTTTTTGATAAGATATAATTTA
1 GTTTTTGATAAGATATAATTTA
13906 GTTTTTGATAAGATAT-ATTTA
1 GTTTTTGATAAGATATAATTTA
*
13927 CTTTTTGATAA
1 GTTTTTGATAA
13938 ATTATTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (22 bp):
GTTTTTGATAAGATATAATTTA
Found at i:13946 original size:22 final size:22
Alignment explanation
Indices: 13885--13947 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
13875 GTTGACCATG
* *
13885 TTTTTGATAAGATATAATTTAG
1 TTTTTGATAAGATATTATTTAC
13907 TTTTTGATAAGATA-TATTTAC
1 TTTTTGATAAGATATTATTTAC
13928 TTTTTGATAA-ATTATTATTT
1 TTTTTGATAAGA-TATTATTT
13948 TATTATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.03
21 17 0.46
22 19 0.51
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTTTGATAAGATATTATTTAC
Found at i:15821 original size:15 final size:16
Alignment explanation
Indices: 15793--15826 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
15783 ATTTTTAGAA
15793 TTTTATTTAAATTTATT
1 TTTTATTT-AATTTATT
15810 TTTTATTT-ATTTATT
1 TTTTATTTAATTTATT
15825 TT
1 TT
15827 GACTAGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATTTAATTTATT
Found at i:16156 original size:9 final size:8
Alignment explanation
Indices: 16131--16155 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16121 GCAAATAGAG
16131 AGAAAAAA
1 AGAAAAAA
16139 AGAAAAAA
1 AGAAAAAA
16147 AGAAAAAA
1 AGAAAAAA
16155 A
1 A
16156 ATAAGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:19698 original size:15 final size:16
Alignment explanation
Indices: 19673--19709 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
19663 TACTACATAA
19673 AAAAAACATTAATA-TG
1 AAAAAACATTAA-ACTG
19689 AAAAAA-ATTAAACTG
1 AAAAAACATTAAACTG
19704 AAAAAA
1 AAAAAA
19710 TAAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 13 0.65
16 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.19
Consensus pattern (16 bp):
AAAAAACATTAAACTG
Found at i:20476 original size:16 final size:17
Alignment explanation
Indices: 20455--20492 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
20445 TATATTAATT
20455 ATTTAAAATTAAAAT-A
1 ATTTAAAATTAAAATAA
*
20471 ATTT-AAATTTAAATAA
1 ATTTAAAATTAAAATAA
20487 ATTTAA
1 ATTTAA
20493 CTCAAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 9 0.47
17 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTAAAATTAAAATAA
Found at i:20484 original size:15 final size:16
Alignment explanation
Indices: 20455--20492 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20445 TATATTAATT
20455 ATTTAAAATTAAAAT-A
1 ATTT-AAATTAAAATAA
*
20471 ATTTAAATTTAAATAA
1 ATTTAAATTAAAATAA
20487 ATTTAA
1 ATTTAA
20493 CTCAAAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTAAAATAA
Found at i:20531 original size:13 final size:14
Alignment explanation
Indices: 20513--20541 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20503 TTTCAACTTG
20513 AATTAATTT-AAAT
1 AATTAATTTGAAAT
20526 AATTAATTTGAAAT
1 AATTAATTTGAAAT
20540 AA
1 AA
20542 CACGAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATTAATTTGAAAT
Found at i:26658 original size:11 final size:11
Alignment explanation
Indices: 26642--26672 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
26632 ATAAAATTAC
26642 ATAATTAAAAT
1 ATAATTAAAAT
26653 ATAATTAAAAT
1 ATAATTAAAAT
*
26664 ATAAATAAA
1 ATAATTAAA
26673 CATGTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAATTAAAAT
Found at i:27690 original size:32 final size:33
Alignment explanation
Indices: 27653--27714 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
27643 ATTTTTAATA
*
27653 TATAATTAAT-TAT-TATTTATAAACATAATTTT
1 TATAATTAATATATATATATATAAA-ATAATTTT
27685 TATAATTAATATATATATATATAAAATAAT
1 TATAATTAATATATATATATATAAAATAAT
27715 CTCATTATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 10 0.37
33 8 0.30
34 9 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
TATAATTAATATATATATATATAAAATAATTTT
Found at i:30044 original size:21 final size:21
Alignment explanation
Indices: 29989--30047 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
29979 TGATCTATAG
*
29989 ATACATTAGATTAATGTATCG
1 ATACATTAGATTAATGTATCC
* **
30010 ATATATCT-TTTTAATGTATCC
1 ATACAT-TAGATTAATGTATCC
*
30031 ATACATTAGGTTAATGT
1 ATACATTAGATTAATGT
30048 TTTGTTACAT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (21 bp):
ATACATTAGATTAATGTATCC
Found at i:36051 original size:21 final size:18
Alignment explanation
Indices: 36014--36053 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 18
36004 AAGTTATATC
36014 AATAATTTATTTTTTAAA
1 AATAATTTATTTTTTAAA
36032 AATAATGTTATATATTTTAAA
1 AATAAT-TTAT-T-TTTTAAA
36053 A
1 A
36054 TCTACTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 1 0.05
21 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATAATTTATTTTTTAAA
Found at i:41280 original size:52 final size:52
Alignment explanation
Indices: 41195--41319 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
41185 ATATGAAAAG
* *
41195 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
41247 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
41299 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
41320 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:41332 original size:52 final size:51
Alignment explanation
Indices: 41195--41339 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
41185 ATATGAAAAG
*
41195 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
41247 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
41299 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
41340 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:41346 original size:13 final size:13
Alignment explanation
Indices: 41328--41352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41318 CAAAGATCAG
41328 TGTATCGATACAA
1 TGTATCGATACAA
41341 TGTATCGATACA
1 TGTATCGATACA
41353 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:42460 original size:28 final size:28
Alignment explanation
Indices: 42420--42491 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
42410 GAAAAAAAAT
* ** *
42420 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
42448 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
42476 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
42492 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:42611 original size:52 final size:52
Alignment explanation
Indices: 42481--42649 Score: 148
Period size: 52 Copynumber: 3.2 Consensus size: 52
42471 AATAACGAGG
* * * * *
42481 TTGGAGTATCCTCGATTG-TGAAAAATTGGTATTTTTGGAAATAGAATC-GGA
1 TTGGAGTATCCCCGATTGAGGAAAAATTGG-AGTTTTGAAAATAAAATCGGGA
* * * *
42532 GTTGGAATATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCGGGA
1 -TTGGAGTATCCCCGATT-GAGGAAAAATTGGAGTTTTGAAAATAAAATCGGGA
* * ** *
42585 TTGGAGTATCCCCGATTGAGGAAAAATTAGTGTTTT-AGCGATAAAATCGGGG
1 TTGGAGTATCCCCGATTGAGGAAAAATTGGAGTTTTGA-AAATAAAATCGGGA
42637 TTGGAGTATCCCC
1 TTGGAGTATCCCC
42650 TTGGAAATAA
Statistics
Matches: 95, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
51 4 0.04
52 79 0.83
53 11 0.12
54 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
TTGGAGTATCCCCGATTGAGGAAAAATTGGAGTTTTGAAAATAAAATCGGGA
Found at i:42695 original size:27 final size:29
Alignment explanation
Indices: 42632--42707 Score: 113
Period size: 27 Copynumber: 2.7 Consensus size: 29
42622 GCGATAAAAT
*
42632 CGGGGTTGGAGTATCCCC-TTGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGGAAATAA
*
42660 CGGGGTTGGAGTATCCCCGAT-G-ATTAA
1 CGGGGTTGGAGTATCCCCGATGGAAATAA
42687 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
42708 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.56
28 19 0.42
29 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCCCGATGGAAATAA
Found at i:45198 original size:13 final size:13
Alignment explanation
Indices: 45180--45205 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45170 ACAAAGATCC
45180 ATGTATCGATACA
1 ATGTATCGATACA
45193 ATGTATCGATACA
1 ATGTATCGATACA
45206 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:45201 original size:33 final size:33
Alignment explanation
Indices: 45159--45225 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
45149 AAAATTTCCA
***
45159 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
45192 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
45225 A
1 A
45226 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:45966 original size:55 final size:55
Alignment explanation
Indices: 45883--46835 Score: 1604
Period size: 55 Copynumber: 17.3 Consensus size: 55
45873 ATAAAGTGTA
* * ** * ** *
45883 TCCTGCTCATTGAGGAGTAAAAAATGCCACAAACACGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
45938 TCCTACTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGCG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
45993 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
46048 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
46103 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGACTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
46158 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
46213 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
46268 TCCTGCTCTTTGAGGACTGGAAAATGCCATCAACTTAG-GTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTT-GTGTGGGCTTTGAAAGGTG
46323 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
46378 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
46433 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
46488 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTAG-GTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTT-GTGTGGGCTTTGAAAGGTG
46543 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
46598 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
46653 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
46708 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTAG-GTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTT-GTGTGGGCTTTGAAAGGTG
46763 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
46818 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
46836 AAAAAGCGGA
Statistics
Matches: 865, Mismatches: 15, Indels: 36
0.94 0.02 0.04
Matches are distributed among these distances:
54 16 0.02
55 832 0.96
56 17 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:47822 original size:1 final size:1
Alignment explanation
Indices: 47818--47887 Score: 68
Period size: 1 Copynumber: 70.0 Consensus size: 1
47808 CTTTTCTCTC
* * * * ** **
47818 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTTGCTTTTTTTTTTTTGCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47883 TTTTT
1 TTTTT
47888 GAAGAGAAGG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.04, G:0.07, T:0.89
Consensus pattern (1 bp):
T
Found at i:47836 original size:14 final size:14
Alignment explanation
Indices: 47817--47886 Score: 90
Period size: 14 Copynumber: 4.9 Consensus size: 14
47807 TCTTTTCTCT
47817 CTTTTTCTTTGTTTTG
1 CTTTTT-TTT-TTTTG
47833 -TTTTTTTGTTTTT-
1 CTTTTTTT-TTTTTG
*
47846 TTTTTTTTTTTTTG
1 CTTTTTTTTTTTTG
47860 CTTTTTTTTTTTTG
1 CTTTTTTTTTTTTG
47874 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
47887 TGAAGAGAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
13 5 0.10
14 39 0.78
15 6 0.12
ACGTcount: A:0.00, C:0.06, G:0.07, T:0.87
Consensus pattern (14 bp):
CTTTTTTTTTTTTG
Found at i:47870 original size:33 final size:32
Alignment explanation
Indices: 47818--47887 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
47808 CTTTTCTCTC
*
47818 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTT
1 TTTTTCTTTGTTTTGTTTTTTTGCTTTTTTTT
* *
47850 TTTTTTTTTGCTTTTTTTTTTTTGCTTTTTTTT
1 TTTTTCTTTG-TTTTGTTTTTTTGCTTTTTTTT
47883 TTTTT
1 TTTTT
47888 GAAGAGAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 9 0.26
33 25 0.74
ACGTcount: A:0.00, C:0.04, G:0.07, T:0.89
Consensus pattern (32 bp):
TTTTTCTTTGTTTTGTTTTTTTGCTTTTTTTT
Done.