Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018284.1 Corchorus olitorius cultivar O-4 contig18317, 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: 190247
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1023 original size:26 final size:26
Alignment explanation
Indices: 994--1048 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
984 ATGTTGGAAA
994 GATGACAAATGTTGTCAATTTGGATT
1 GATGACAAATGTTGTCAATTTGGATT
1020 GATGACAAATGTTGTCAATTTGGATT
1 GATGACAAATGTTGTCAATTTGGATT
1046 GAT
1 GAT
1049 AAGGGGGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (26 bp):
GATGACAAATGTTGTCAATTTGGATT
Found at i:1466 original size:37 final size:37
Alignment explanation
Indices: 1421--1911 Score: 421
Period size: 37 Copynumber: 13.4 Consensus size: 37
1411 TTCAATATTT
*
1421 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGATCC
* * *
1458 CTGCTTAGGTGT-TTCATCAAAAT-CTTATTCAAGATTC
1 CTGTTTAGGTGTCTT-ATC-AAATCCTTATTTAAGATCC
* *
1495 CTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGATCC
*
1532 CTGTTTAGGTGTCTAATCAAATCCTTATTTAAG----
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGATCC
** ** * *
1565 --GTTTAGGTGTCACATCGAAAT-CTGGTTCAAGATCT
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGATCC
* * *
1600 CTGTTTAGGTGTCTCATCAAAAT-CTTATTCAAGATTC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGATCC
* * *
1637 CTGTTTAGGTTTCTTATTAAATCTTTATTTAAGATCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGATCC
* * *
1674 CTATTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATCC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGATCC
* * * *
1711 ATGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTGC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGATCC
* * ** * *
1748 CTGTTTAGGTTTCTTGTCAAAATTTTTGTTTAAGATCA
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGATCC
* * *
1786 CTGTTTAGATTTCTTATCAAATCCTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGATCC
* * * * *
1823 CTGTTTAGGTGTCTCATCAAAAT-CTTGTTCAAAATTC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGATCC
* * * *
1860 CTGTTTAGGCTTTCTTATTAAATCCTTATTTAAGGTAC
1 CTGTTTAGG-TGTCTTATCAAATCCTTATTTAAGATCC
*
1898 TTGTTTAGGTGTCT
1 CTGTTTAGGTGTCT
1912 CTTCAAAATC
Statistics
Matches: 362, Mismatches: 74, Indels: 36
0.77 0.16 0.08
Matches are distributed among these distances:
31 21 0.06
32 4 0.01
36 14 0.04
37 257 0.71
38 66 0.18
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.44
Consensus pattern (37 bp):
CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGATCC
Found at i:1499 original size:74 final size:74
Alignment explanation
Indices: 1394--1921 Score: 590
Period size: 74 Copynumber: 7.2 Consensus size: 74
1384 ACAAAATTCA
* * * *
1394 GTCTCATCAAAACCTTGTTCAATATTTCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
1459 TGCTTAGGT
66 TGTTTAGGT
* * * *
1468 GTTTCATCAAAATCTTATTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
1533 TGTTTAGGT
66 TGTTTAGGT
* * * * ** ** * *
1542 GTCTAATC-AAATCCTTATTTAAG------GTTTAGGTGTCACATCGAAAT-CTGGTTCAAGATC
1 GTCTCATCAAAAT-CTTGTTCAAGATTCCTGTTTAGGTTTCTTATC-AAATCCTTATTTAAGGTC
*
1599 TCTGTTTAGGT
64 CCTGTTTAGGT
* * * *
1610 GTCTCATCAAAATCTTATTCAAGATTCCTGTTTAGGTTTCTTATTAAATCTTTATTTAAGATCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
1675 TATTTAGGT
66 TGTTTAGGT
* *
1684 GTCTCATCAAAATCTTGTTTAAGA-TCCATGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTGC
1 GTCTCATCAAAATCTTGTTCAAGATTCC-TGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCC
1748 CTGTTTAGGT
65 CTGTTTAGGT
* ** * * *
1758 TTCTTGTCAAAATTTTTGTTTAAGA-TCACTGTTTAGATTTCTTATCAAATCCTTATTTAAGGTC
1 GTCTCATCAAAA-TCTTGTTCAAGATTC-CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTC
1822 CCTGTTTAGGT
64 CCTGTTTAGGT
* * *
1833 GTCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGCTTTCTTATTAAATCCTTATTTAAGGTAC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGG-TTTCTTATCAAATCCTTATTTAAGGTCC
*
1898 TTGTTTAGGT
65 CTGTTTAGGT
*
1908 GTCTCTTCAAAATC
1 GTCTCATCAAAATC
1922 CCAGTTTAGG
Statistics
Matches: 387, Mismatches: 52, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
68 50 0.13
69 8 0.02
73 11 0.03
74 201 0.52
75 116 0.30
76 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (74 bp):
GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
TGTTTAGGT
Found at i:1705 original size:142 final size:143
Alignment explanation
Indices: 1423--1851 Score: 463
Period size: 142 Copynumber: 3.0 Consensus size: 143
1413 CAATATTTCT
** * * * * * *
1423 GTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGCTTAGGTGTTTCATCAAAATCTTATTC
1 GTTTAGGTGTCACATCAAATCCTGATTCAAGATGCCTGTTTAGGTGTCTCATCAAAATCTTATTC
* * *
1488 AAGATTCCTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTAATC-AA
66 AAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAA
*
1552 ATCCTTATTTAAG-
131 AT-CTTGTTTAAGA
*
1565 GTTTAGGTGTCACATCGAAAT-CTGGTTCAAGAT-CTCTGTTTAGGTGTCTCATCAAAATCTTAT
1 GTTTAGGTGTCACATC-AAATCCTGATTCAAGATGC-CTGTTTAGGTGTCTCATCAAAATCTTAT
* * * *
1628 TCAAGATTCCTGTTTAGGTTTCTTATTAAATCTTTATTTAAGATCCCTATTTAGGTGTCTCATCA
64 TCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCA
1693 AAATCTTGTTTAAGATCCA
129 AAATCTTGTTTAAG----A
* ** * * * * ** * *
1712 TGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTGCCTGTTTAGGTTTCTTGTCAAAATTTTTGT
1 -GTTTAGGTGTCACATCAAATCCTGATTCAAGATGCCTGTTTAGGTGTCTCATCAAAA-TCTTAT
* *
1777 TTAAGA-TCACTGTTTAGATTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATC
64 TCAAGATTC-CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATC
1841 AAAATCTTGTT
128 AAAATCTTGTT
1852 CAAAATTCCT
Statistics
Matches: 240, Mismatches: 34, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
141 1 0.00
142 114 0.47
143 8 0.03
147 4 0.02
148 42 0.17
149 71 0.30
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (143 bp):
GTTTAGGTGTCACATCAAATCCTGATTCAAGATGCCTGTTTAGGTGTCTCATCAAAATCTTATTC
AAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAA
ATCTTGTTTAAGA
Found at i:1720 original size:179 final size:179
Alignment explanation
Indices: 1410--1911 Score: 472
Period size: 179 Copynumber: 2.8 Consensus size: 179
1400 TCAAAACCTT
* * * * *
1410 GTTCAATATTTCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGCTTAGGTGTTTCAT
1 GTTCAAGATCTCTGTTTAGGTGTCTCATCAAATCCTTATTCAAGATCCCTGCTTAGGTGTTTCAT
* * * * *
1475 CAAAATCTTATTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGGTCCCTGTTTAG
66 CAAAATCTTATTCAAGATCCCTATTTAGGTGTCTCATCAAATCCTTGTTTAAGATCCATGTTTAG
1540 GTGTCTAATCAAATCCTTATTTAAGGTTTAGGTGTCACATCGAAATCTG
131 GTGTCTAATCAAATCCTTATTTAAGGTTTAGGTGTCACATCGAAATCTG
* * *
1589 GTTCAAGATCTCTGTTTAGGTGTCTCATCAAAAT-CTTATTCAAGATTCCTGTTTAGGT-TTCTT
1 GTTCAAGATCTCTGTTTAGGTGTCTCATC-AAATCCTTATTCAAGATCCCTGCTTAGGTGTT-TC
* *
1652 AT-TAAATCTTTATTTAAGATCCCTATTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATCCATGT
64 ATCAAAATC-TTATTCAAGATCCCTATTTAGGTGTCTCATC-AAATCCTTGTTTAAGATCCATGT
* * * *** * * *
1715 TTAGGTTTCTTATCAAATCCTTATTTAAGGTGCCTGTTTAGGTTTCTTGTCAAAATTTTT
127 TTAGGTGTCTAATCAAATCCTTATTTAA---G---GTTTAGGTGTCACATCGAAA-TCTG
* * * * * * * * *
1775 GTTTAAGATCACTGTTTAGATTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCAT
1 GTTCAAGATCTCTGTTTAGGTGTCTCATCAAATCCTTATTCAAGATCCCTGCTTAGGTGTTTCAT
* * * * * * * * * * *
1840 CAAAATCTTGTTCAAAATTCCTGTTTAGGCTTTCTTATTAAATCCTTATTTAAGGTACTTGTTTA
66 CAAAATCTTATTCAAGATCCCTATTTAGG-TGTCTCATCAAATCCTTGTTTAAGATCCATGTTTA
1905 GGTGTCT
130 GGTGTCT
1912 CTTCAAAATC
Statistics
Matches: 259, Mismatches: 48, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
178 7 0.03
179 118 0.46
180 8 0.03
182 1 0.00
185 19 0.07
186 71 0.27
187 35 0.14
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.44
Consensus pattern (179 bp):
GTTCAAGATCTCTGTTTAGGTGTCTCATCAAATCCTTATTCAAGATCCCTGCTTAGGTGTTTCAT
CAAAATCTTATTCAAGATCCCTATTTAGGTGTCTCATCAAATCCTTGTTTAAGATCCATGTTTAG
GTGTCTAATCAAATCCTTATTTAAGGTTTAGGTGTCACATCGAAATCTG
Found at i:2207 original size:33 final size:33
Alignment explanation
Indices: 2165--2242 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
2155 ATTAATTAAG
* * * *
2165 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
2198 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
2231 AAGTTCAAAATC
1 AAGTTCAAAATC
2243 CACAGTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:2770 original size:7 final size:7
Alignment explanation
Indices: 2399--2768 Score: 490
Period size: 7 Copynumber: 51.9 Consensus size: 7
2389 AATAGGCAAT
*
2399 TCAAAAT
1 TCAAAAC
*
2406 TCAAAAT
1 TCAAAAC
*
2413 TCAAAAT
1 TCAAAAC
2420 TCAAAAC
1 TCAAAAC
2427 TCAAAAC
1 TCAAAAC
2434 TCAAAAC
1 TCAAAAC
2441 TCAAAAC
1 TCAAAAC
2448 TCAAAAC
1 TCAAAAC
2455 TCAAAAC
1 TCAAAAC
2462 TCAAAAC
1 TCAAAAC
2469 TCAAAAC
1 TCAAAAC
2476 TCAAAAC
1 TCAAAAC
2483 TCAAAAC
1 TCAAAAC
2490 TCAAAAC
1 TCAAAAC
2497 TCAAAAC
1 TCAAAAC
2504 TCAAAAC
1 TCAAAAC
2511 TCAAAAC
1 TCAAAAC
2518 TCAAAAC
1 TCAAAAC
2525 TCAAAAC
1 TCAAAAC
2532 TCAAAAC
1 TCAAAAC
2539 TCAAAAC
1 TCAAAAC
2546 TCAAAAC
1 TCAAAAC
2553 TCAAAAC
1 TCAAAAC
2560 TCAAAAC
1 TCAAAAC
2567 TCAAAAC
1 TCAAAAC
2574 TCAAAAC
1 TCAAAAC
2581 TCAAAAC
1 TCAAAAC
2588 TCAAAAAGC
1 TC-AAAA-C
2597 TCAAAAC
1 TCAAAAC
2604 TCAAAAC
1 TCAAAAC
2611 TCAAAAAC
1 TC-AAAAC
2619 TCAAAAC
1 TCAAAAC
2626 TCAAAAAC
1 TC-AAAAC
2634 TCAAAA-
1 TCAAAAC
*
2640 TCATCAAAT
1 TCA--AAAC
*
2649 TACAAAAT
1 T-CAAAAC
2657 TCAAAAAC
1 TC-AAAAC
*
2665 TCAAAAT
1 TCAAAAC
*
2672 TCAAAAT
1 TCAAAAC
*
2679 TCAAAAT
1 TCAAAAC
*
2686 TCAAAAT
1 TCAAAAC
*
2693 TCAAAAT
1 TCAAAAC
*
2700 TCAAAAT
1 TCAAAAC
*
2707 TCAAAAT
1 TCAAAAC
*
2714 TCAAAAT
1 TCAAAAC
*
2721 TCAAAAT
1 TCAAAAC
*
2728 TCAAAAT
1 TCAAAAC
*
2735 TCAAAAT
1 TCAAAAC
*
2742 TCAAAAT
1 TCAAAAC
*
2749 TCAAAAT
1 TCAAAAC
*
2756 TCAAAAT
1 TCAAAAC
2763 TCAAAA
1 TCAAAA
2769 TTTGCATTTT
Statistics
Matches: 351, Mismatches: 3, Indels: 18
0.94 0.01 0.05
Matches are distributed among these distances:
6 3 0.01
7 306 0.87
8 36 0.10
9 4 0.01
10 2 0.01
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (7 bp):
TCAAAAC
Found at i:2816 original size:27 final size:27
Alignment explanation
Indices: 2755--2823 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
2745 AAATTCAAAA
* * *
2755 TTCAAAATTCAAAATTTGCATTTTTAT
1 TTCAAAACTCAAAATTTGCATTGTCAT
2782 TTCAAAACTCAAAATTTGCA-TGTCAT
1 TTCAAAACTCAAAATTTGCATTGTCAT
*
2808 GTTCGAAACTCAAAAT
1 -TTCAAAACTCAAAAT
2824 CCAGAGTCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 4 0.11
27 33 0.89
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (27 bp):
TTCAAAACTCAAAATTTGCATTGTCAT
Found at i:7440 original size:315 final size:311
Alignment explanation
Indices: 6802--8114 Score: 1132
Period size: 315 Copynumber: 4.2 Consensus size: 311
6792 CCCAAAACAA
* * * *
6802 TGGCAGAGATTTCGTTAGATGAATATAGATATTTCAGGGAGTCTTTATGCCAAAAATCATGCAAA
1 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTA-GCCAAAAACCATGCAAA
* * * * * * *
6867 ACTGAGCGGGGGCCCCAAAACGCCTTTTTAGCCCCAAAACCGTGATGGTTAGTACACGATTTCGG
65 ATTAAGCCGGCG-CCCGAAACGCGTTTTTAG--CAAAAACCGTGATGGTTAG-ACA--ATTTC-G
* * * *
6932 CTAAAAACTAACCCGAAAAATTTTTTCCTGAATTTTTTCCCACAATACTCAGAAAAAATATATAA
123 C-AAAAACTAACCC--AAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAA
* * * * *
6997 TTCAACGTCAAAAAGATT-AACAGGCTTCTCACGCTTCT-A-ATCGTTTTTTTTTTCCTTTTTTC
185 TTCAACGCCAAAAAGATTGAA-GGGTTTTTCACGCTTCTAATATCG--TTTTTCTT--TTTTTTC
* * * * * ** * *
7059 CAAATTAATTTCCAATTAAATAGAAATAAGATTCAGATGCTCGTAAGAACAAATTCTTATATCCA
245 CAAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGAACGTAA-AACAAATCCTTAAATCCA
7124 ATG
309 ATG
* * * *
7127 TGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTGAGGCAAAAATCATGCAAA
1 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-AGCCAAAAACCATGCAAA
* * * * *
7192 ATTAAGCCGGCGCTCCGGAATGCGTTTTTAACTAAAAACCGTGAT-GCTA-A-AATTTTGCAAAA
65 ATTAAGCCGGCGC-CCGAAACGCGTTTTTAGC-AAAAACCGTGATGGTTAGACAATTTCGCAAAA
* * *
7254 ACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAAATAAATAATTCAAC
128 ACTAACCC-AAAAGTTTTTCCTCAATTTTTTGCCACAATACTCA-TAAAAAATATATAATTCAAC
* * *
7319 GCCAAAAAAATTGAAGGGTTATTCACGCTGCTAATATCGTTTTTCGTTTTTTTTCCCAAATTTAT
191 GCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTC-TTTTTTTT-CCAAATTTAT
* *
7384 TTCTAA-TAAATCGAAATAAGATTCAAATGAAAC-TAAAAGCGAATCCTTAAATCCAATG
254 TTCTAATTAAATCGAAACAAGATTCAAATG-AACGTAAAA-CAAATCCTTAAATCCAATG
* * *
7442 TGGCTGAGATTTGGTTAGTTGAATATATATATTTCAAGGAGCCTTTAAGCCAAAAACCATGCAAA
1 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-AGCCAAAAACCATGCAAA
* * *
7507 ACTGAGTCGAG-GCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGG
65 ATTAAGCCG-GCGCCC-GAAACGCGTTTTTAG-CAAAAACCGTGATGGTTAG-ACA--ATTTC-G
* **** ** ** *
7571 CTAAAA-TTTTGCAAAA--ACTAACTCGAA--ATTTGCCACAATACTCATAAAAAATATATAATT
123 CAAAAACTAACCCAAAAGTTTTTCCTC-AATTTTTTGCCACAATACTCATAAAAAATATATAATT
* * * ** *
7631 CAAGGCCAAAAATATTGAAGGGTTTTTCATGCTTCTAATATCGTTTTTC-CATTTTTCTAGAATT
187 CAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTCCA-AATT
* *
7695 TATTTCTAATT-AATCCAAACAAG------AT--A---AAAACAAATCCTTCAATCCAATG
251 TATTTCTAATTAAATCGAAACAAGATTCAAATGAACGTAAAACAAATCCTTAAATCCAATG
* *
7744 TGGCTGAGATTTGTTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAACCATTCAAT
1 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTA-GCCAAAAACCATGCAA-
* * * ** * * * *
7809 ACTGAGGTGAGGCGCCCGAAACGTCTTTTTTTGCGAAAACCTGTGATGGTTAGTACCCGATTTCG
64 AATTAAG-CCGGCGCCCGAAACG-CGTTTTTAGCAAAAACC-GTGATGGTTAG-A--CAATTTCG
* *
7874 GATAAAACTAACCCAAATAGTTTTTTCTCAATTTTTTTGCCACAATACTCATAAAAAATATATAA
123 CA-AAAACTAACCCAAA-AGTTTTTCCTCAA-TTTTTTGCCACAATACTCATAAAAAATATATAA
* * * * * *
7939 TTGAATGCCAAAAAGATTTAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCATTTTTTTCCGAA
185 TTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-CTTTTTTTTCCAAA
* ** *
8004 TTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATG
249 TTTATTTCTAATTAAATCGAAACAAGATTCAAATGAACGT-AAAACAAATCCTTAAATCCAATG
* * *
8068 TGGCTGGGATTTGGTTCGATGAATATAGATATTTCAAGAAGTCTTTA
1 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTA
8115 TGTGATCCCT
Statistics
Matches: 808, Mismatches: 125, Indels: 111
0.77 0.12 0.11
Matches are distributed among these distances:
301 1 0.00
302 74 0.09
303 21 0.03
304 34 0.04
305 6 0.01
306 2 0.00
307 2 0.00
308 6 0.01
310 76 0.09
311 16 0.02
312 17 0.02
313 2 0.00
314 32 0.04
315 168 0.21
316 134 0.17
317 23 0.03
318 15 0.02
319 3 0.00
320 5 0.01
321 7 0.01
322 6 0.01
323 4 0.00
324 76 0.09
325 77 0.10
326 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (311 bp):
TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTAGCCAAAAACCATGCAAAA
TTAAGCCGGCGCCCGAAACGCGTTTTTAGCAAAAACCGTGATGGTTAGACAATTTCGCAAAAACT
AACCCAAAAGTTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCCAA
AAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTCCAAATTTATTTCTAAT
TAAATCGAAACAAGATTCAAATGAACGTAAAACAAATCCTTAAATCCAATG
Found at i:9735 original size:328 final size:323
Alignment explanation
Indices: 8559--10147 Score: 1306
Period size: 328 Copynumber: 4.9 Consensus size: 323
8549 AAAATTTTGC
* * *
8559 AAAAACTAACCCG-AAAACTTTTTCCTCAATTTTTTTTGCCACAACAGC-C-ATAAAAAATATAT
1 AAAAACTGA-CCGAAAAATTTTTTCCTCAA-TTTTTTTGCCACAATA-CTCTA-AAAAAATATAT
** *
8621 AATTCAATGCAAAAAAAAAAGTTGAAGGGTTTTTTACG-ATTCTAATATCG-TTTT--TTATTTT
62 AATTCAA--CACCAAAAAAA-TTGAAGGGTTTTTCACGCA-TCTAATATCGTTTTTCCTTATTTT
* * * *
8682 TTTCAGAATTTATTTCTAATTAAATCG-AACCAGTCTTCAGATGCTCGTAAAAACAAATCCTAAA
123 TTTCCGAATTTATTTCTAATTAAATCGAAACAAG-ATTCAGATGCTCGTAAAAACAAATCCTTAA
* * * *
8746 ATCCAACGTAGCTAAGATTT-GTTATATATATATATATATATTTCAAGGAGTCTTT-CTACCAAA
187 ATCCAATGT-GCTAAGATTTGGTTAGAT-GA-ATATAGATATTTCAAGGAGTCTTTAC-ACCAAA
* * * * * * *
8809 AGTCATGGTAAATTGAGTTGGGGCTCCGGAACGCGTTTTTAGCCCAAAAACCGTGATGGTTAGTA
248 AATCATGGAAAACTGAGTCGGGGCTCCGAAACGCATTTTTAG-CCAAAAACCGTGATGATTAGTA
*
8874 TACGATTTCGTCT
312 -ACGATTTCGGCT
* * * * * * *
8887 TAAAACTGACATG-AAATTTTTTTTCTGACATTTTTGTT---ATAGTACT-TAGAAAAAATATAT
1 AAAAACTGAC-CGAAAAATTTTTTCCTCA-ATTTTT-TTGCCACAATACTCTA-AAAAAATATAT
* * * * * *
8947 AATTCATCGCCAATAAGATTGACGGGTTTTTCACG-ATCTAATATCATTTTTCC--ATTTTTTT-
62 AATTCAACACCAAAAAAATTGAAGGGTTTTTCACGCATCTAATATCGTTTTTCCTTATTTTTTTC
* * * * * *
9008 CAAATTAATTTCTGATTAAATCGAAACAAGATTCATATGCTTGTAAAAACAAATCCTTATATCCA
127 CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCA
* * *
9073 ATGTGGCTGAA-ATTTGGTTCGATGAGTATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATG
192 ATGT-GCT-AAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAATCATG
* * * * *
9137 GAAAATTGAGTCGGGGCTCCGGAACGCATTTTTAGTCAAAAACCATGATGGTCT-GTAAACGATT
255 GAAAACTGAGTCGGGGCTCCGAAACGCATTTTTAGCCAAAAACCGTGATGAT-TAGT-AACGATT
9201 TCGGCTAAAATTTT
318 TCGGC--------T
* ** * * ** * * *
9215 GCAAAAACTGACTG-GTAATGTTTTTCCTCAATTTGTTTGCTATTATACTC-AGAAAATTATATG
1 --AAAAACTGACCGAAAAAT-TTTTTCCTCAATTTTTTTGCCACAATACTCTAAAAAAATATATA
* * * * * * *
9278 GTTTAACGCCAAAAAAGTTGAAGGATTTTTCACGCTTATAATATCGTTTTTCC--ATTTTTTTCC
63 ATTCAACACCAAAAAAATTGAAGGGTTTTTCACGCATCTAATATCGTTTTTCCTTATTTTTTTCC
* *
9341 GAATTTATTTCTAATTAAATCGAAATAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAA
128 GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* *
9406 TGTGCCTAAGATTTGGTTAGATGAATATAGATACTTT-AAGGAGTCTTTATACCAAAAACCATGG
193 TGTG-CTAAGATTTGGTTAGATGAATATAGATA-TTTCAAGGAGTCTTTACACCAAAAATCATGG
* * * *
9470 AAAACTGAGTCGAGGC-CCTAAAATGCATTTTTAG-CAAAAACTGTGATGATTAGTACACGATTT
256 AAAACTGAGTCGGGGCTCC-GAAACGCATTTTTAGCCAAAAACCGTGATGATTAGTA-ACGATTT
9533 CGGCT
319 CGGCT
* *
9538 AAAAACTGATCCGAAAAATTCTTT-CTCAATTTTTTTGTCACAATACTCATAAAAAAATATATAA
1 AAAAACTGA-CCGAAAAATTTTTTCCTCAATTTTTTTGCCACAATACTC-TAAAAAAATATATAA
9602 TTCAACACCAAAAAAATTGAAGGGTTTTTCACGCATCTAATATCGTTTTTCCATATATATTTTTT
64 TTCAACACCAAAAAAATTGAAGGGTTTTTCACGCATCTAATATCGTTTTTCC-T-TAT-TTTTTT
* **
9667 CCGAATTTATTTCTAATTAAATCGAAAAAAGATTCAGATGCTCGTAAAAGTAAATCCTTAAATCC
126 CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
** * * * *
9732 AATGTAGCTGGGATTTGGTTAGATAAATATAGATATTTCAAGAATTCTTTACACTAAAAATCATG
191 AATGT-GCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAATCATG
* * * * *
9797 CAAAACTGAGCCGGGGCCCCGAAATGCCTTTTT--------A-C----T-A-TAG----GATTTC
255 GAAAACTGAGTCGGGGCTCCGAAACGCATTTTTAGCCAAAAACCGTGATGATTAGTAACGATTTC
9843 GGCT
320 GGCT
* ** * * *
9847 AAAAATTGAGCCGAAATTTTTTTTTCCTGAA--TTTTTGCCACAATAATCTAAAAAAATATATTA
1 AAAAACTGA-CCGAAA-AATTTTTTCCTCAATTTTTTTGCCACAATACTCTAAAAAAATATATAA
* * *
9910 TTCAACACCAAAAAGATTGAAGGGTTTTTCACACTTCTAATATCGTTTTTCCTT-TTTTTTT--G
64 TTCAACACCAAAAAAATTGAAGGGTTTTTCACGCATCTAATATCGTTTTTCCTTATTTTTTTCCG
* ** * * *
9972 AATTTATTTCTAATTAAATCGATACTTGATTCAAATGCTCGTAAAAACATATGCTTAAATCCAAT
129 AATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
** * * * * * * * *
10037 GTGGCTGGGATTTGGTTTGATGAATATAAATATTCCAAGAAGACTTTACGCCAAAAATGATGCAA
194 GT-GCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAATCATGGAA
* * *
10102 AACTGAGCTC-GGGCGCCGAAACGCGTTTTTAGCAAAAAACCGTGAT
258 AACTGAG-TCGGGGCTCCGAAACGCATTTTTAGCCAAAAACCGTGAT
10148 AGCACTTCAA
Statistics
Matches: 1036, Mismatches: 160, Indels: 143
0.77 0.12 0.11
Matches are distributed among these distances:
302 136 0.13
303 1 0.00
304 6 0.01
305 1 0.00
306 1 0.00
307 1 0.00
308 63 0.06
309 39 0.04
310 6 0.01
311 5 0.00
314 3 0.00
315 2 0.00
316 1 0.00
320 27 0.03
321 97 0.09
322 76 0.07
323 100 0.10
324 6 0.01
325 1 0.00
326 21 0.02
327 6 0.01
328 170 0.16
329 15 0.01
330 54 0.05
331 61 0.06
332 134 0.13
333 3 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (323 bp):
AAAAACTGACCGAAAAATTTTTTCCTCAATTTTTTTGCCACAATACTCTAAAAAAATATATAATT
CAACACCAAAAAAATTGAAGGGTTTTTCACGCATCTAATATCGTTTTTCCTTATTTTTTTCCGAA
TTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
GCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAATCATGGAAAAC
TGAGTCGGGGCTCCGAAACGCATTTTTAGCCAAAAACCGTGATGATTAGTAACGATTTCGGCT
Found at i:10383 original size:281 final size:282
Alignment explanation
Indices: 9878--10428 Score: 689
Period size: 281 Copynumber: 2.0 Consensus size: 282
9868 TTTTCCTGAA
* * *
9878 TTTTTGCCACAATAATCTAAAAAAATATATTATTCAACACCAAAAAGATTGAAGGGTTTTTCACA
1 TTTTTGCCACAATAATCTAAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTGCACA
* ** * * * **
9943 CTTCTAATATCGTTTTTCCTTTTTTTTTGAATTTATTTCTAATTAAATCGATACTTGATTCAAAT
66 CTTCTAATATCGTTTTTCCTTTCTTTCCGAATTAACTTCTAATTAAATCGAAACAAGATTCAAAT
* * * * * *
10008 GCTCGTAAAAACATATGCTTAAATCCAATGTGGCTGGGATTTGGTTTGATGAATATAAATATTCC
131 GCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGCTTCGATGAATATAAATATTCC
* *
10073 AAGAAGACTTTACGCCAAAAATGATGCAAAACTGAGCTCGGGCGC-C-GAAACGCGTTTTTAGCA
196 AAGAAGACTTTACACCAAAAATCATGCAAAACTGAG-TCGGG-GCTCTGAAACGCGTTTTTAGCA
10136 AAAAACCGTGATAGCACTTCAATT
259 AAAAACCGTGATAGCACTTCAATT
* * * * * *
10160 TTTTTGCCACCATAGTC-AGAAAAATATATAATTGAACA-CAAAAAAATTTAAGGGTTTTGCACG
1 TTTTTGCCACAATAATCTAAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTGCACA
* *
10223 CTTCTATTATCGTTTTT-CTACTTCTTTCCGAATTAACTTCTAATTAAATCGAAACAAGATTCAT
66 CTTCTAATATCGTTTTTCCT--TTCTTTCCGAATTAACTTCTAATTAAATCGAAACAAGATTCAA
* * *
10287 ATGCTTATAAAAATAAATCCTTATATCCAATGTGGCTGAGATTTGCTTCGATGAATATAAATATT
129 ATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGCTTCGATGAATATAAATATT
** * * * * * *
10352 TTAAGGAGTCTTTGCATCAAAAATCATGCAAAATTGAGTCGGGGCTCTGAAACGCGTTTTTAGCC
194 CCAAGAAGACTTTACACCAAAAATCATGCAAAACTGAGTCGGGGCTCTGAAACGCGTTTTTAGCA
10417 AAAAACCGTGAT
259 AAAAACCGTGAT
10429 GGTTAGTACA
Statistics
Matches: 227, Mismatches: 38, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
279 4 0.02
280 43 0.19
281 165 0.73
282 15 0.07
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (282 bp):
TTTTTGCCACAATAATCTAAAAAAATATATAATTCAACACCAAAAAAATTGAAGGGTTTTGCACA
CTTCTAATATCGTTTTTCCTTTCTTTCCGAATTAACTTCTAATTAAATCGAAACAAGATTCAAAT
GCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGCTTCGATGAATATAAATATTCC
AAGAAGACTTTACACCAAAAATCATGCAAAACTGAGTCGGGGCTCTGAAACGCGTTTTTAGCAAA
AAACCGTGATAGCACTTCAATT
Found at i:10969 original size:324 final size:324
Alignment explanation
Indices: 10154--11010 Score: 913
Period size: 332 Copynumber: 2.6 Consensus size: 324
10144 TGATAGCACT
* * * * * *
10154 TCAATTTTTTTGCCACCATAGTC-AGAAAAATATATAATTGAAC-ACAAAAAAATTTAAGGGTTT
1 TCAA-TTTTTTGCCACAATACTCAAAAAAAATATATAATTTAACGCCAAAAAAATTGAAGGGTTT
* * * * * *
10217 TGCACGCTTCTATTATCGTTTTTCTACTTCTTTCCGAATTAACTTCTAATTAAATCGAAACAAGA
65 TTCACGCTTCTAATATCGTTTTTCT-TTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGA
* ** * * *
10282 TTCATATGCTTATAAAAATAAATCCTTATATCCAATGTGGCTGAGATTTGCTTCGATGAATATAA
129 TTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAG
* * * * ** * * *
10347 ATATTTTAAGGAGTCTTTGCATCAAAAATCATGCAAAATTGAGTCGGGGCTCTGAAACGCGTTTT
194 ATATTTCAACGAGTCTTTACATCAAAAACCATGCAAAATTGAGTCAAGACCCCGAAACGCGTTTT
* * *
10412 TAGCCAAAAACCGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGCAAAAATTGACCCGAAAA
259 TAGCCAAAAACCGTGA-GGTTAGTACACGATTTCAGCTAAAA-TATG----AA-TGACCCAAAAA
*
10477 GTTTTTCC
317 ATTTTTCC
* * * *
10485 TCAATTTTTTGCCATAATACTCAGAAATAATATATAATTTAATGCCAAAAAAATTGAAGGGTTTT
1 TCAATTTTTTGCCACAATACTCAAAAAAAATATATAATTTAACGCCAAAAAAATTGAAGGGTTTT
* * ** *
10550 TCACGCTTCTAATATCATTTTTACATTTTTTTCCAAATTTTTTTCTAATTAAATTGAAACAAGAT
66 TCACGCTTCTAATATCGTTTTT-CTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGAT
* * * *
10615 TCAGATG-TACGTAAAAATAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTAGTATAG
130 TCAGATGCT-CGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAG
** *
10679 ATATTTCAACGAGTCTTTATGTCAAAAACCATGCAAAACTT-AGTCAAGACCCCGAAATGCGTTT
194 ATATTTCAACGAGTCTTTACATCAAAAACCATGCAAAA-TTGAGTCAAGACCCCGAAACGCGTTT
* *
10743 TTAGCCAAAAACCGTGA-GTTAACGTACCCGATTTCGGCTAAAA-ATG-A-G-CCCAAAAAATTT
258 TTAGCCAAAAACCGTGAGGTT-A-GTACACGATTTCAGCTAAAATATGAATGACCCAAAAAATTT
*
10803 TTTC
321 TTCC
*
10807 TCAATTTTTTGCCACAATACTCATAAAAAAAATATATAATTTAACGCCAAAAAGATTGAAGGGTT
1 TCAATTTTTTGCCACAATACTC--AAAAAAAATATATAATTTAACGCCAAAAAAATTGAAGGGTT
* * * **
10872 TTTCACACTTCTAATATCGTTTTTCCTTTTTTTTCCAAATTAATTTCCAATTAAATCAAAATGAG
64 TTTCACGCTTCTAATATCGTTTTT-CTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAG
* ** * * * * * *
10937 ATTTAGATGCTCGTAAAACCATATCCTTAAATCAAATGTGACTGGGATTTAGTTCTATGAATATA
128 ATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATA
11002 GATATTTCA
193 GATATTTCA
11011 CGGAGTTTGT
Statistics
Matches: 437, Mismatches: 79, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
322 34 0.08
323 1 0.00
324 150 0.34
325 2 0.00
330 20 0.05
331 21 0.05
332 206 0.47
333 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (324 bp):
TCAATTTTTTGCCACAATACTCAAAAAAAATATATAATTTAACGCCAAAAAAATTGAAGGGTTTT
TCACGCTTCTAATATCGTTTTTCTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATT
CAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGAT
ATTTCAACGAGTCTTTACATCAAAAACCATGCAAAATTGAGTCAAGACCCCGAAACGCGTTTTTA
GCCAAAAACCGTGAGGTTAGTACACGATTTCAGCTAAAATATGAATGACCCAAAAAATTTTTCC
Found at i:11393 original size:15 final size:16
Alignment explanation
Indices: 11373--11410 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
11363 TATAATATCT
*
11373 TATTATAAT-TAAAAA
1 TATTATAATCGAAAAA
11388 TATTATAATCGAAAAA
1 TATTATAATCGAAAAA
11404 TAATTAT
1 T-ATTAT
11411 TAGAAGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 6 0.30
17 5 0.25
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TATTATAATCGAAAAA
Found at i:11553 original size:20 final size:21
Alignment explanation
Indices: 11515--11556 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11505 TATAATTAAT
*
11515 AAAAAGTTGAATCATCTAAAA
1 AAAAAGTTAAATCATCTAAAA
*
11536 AAAAAGTTAAATGA-CTAAAA
1 AAAAAGTTAAATCATCTAAAA
11556 A
1 A
11557 GAATACTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (21 bp):
AAAAAGTTAAATCATCTAAAA
Found at i:14509 original size:1 final size:1
Alignment explanation
Indices: 14503--14543 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
14493 TTATACATAG
14503 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14544 CTATATCAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14998 original size:17 final size:18
Alignment explanation
Indices: 14976--15015 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
14966 GGACTAATCC
*
14976 TTTAAA-TAAATATATTT
1 TTTAAATTAAATATATTA
*
14993 TTTAAATTAAGTATATTA
1 TTTAAATTAAATATATTA
15011 TTTAA
1 TTTAA
15016 CTAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAAATTAAATATATTA
Found at i:22638 original size:5 final size:5
Alignment explanation
Indices: 22628--22661 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
22618 ACTATTATAC
22628 ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCT
1 ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCT
22662 ATACTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (5 bp):
ATCTT
Found at i:22761 original size:27 final size:28
Alignment explanation
Indices: 22726--22786 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
22716 CTTTTTTTTC
22726 AAAT-ATATTTCTAAAT-TTCCATTACT-
1 AAATAATATTT-TAAATATTCCATTACTA
* *
22752 AAATAATATTTTAATTATTCCATTATTA
1 AAATAATATTTTAAATATTCCATTACTA
22780 AAATAAT
1 AAATAAT
22787 GCAAATTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.27
27 15 0.50
28 7 0.23
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (28 bp):
AAATAATATTTTAAATATTCCATTACTA
Found at i:30505 original size:329 final size:327
Alignment explanation
Indices: 29521--33335 Score: 3075
Period size: 329 Copynumber: 11.5 Consensus size: 327
29511 ATACTTTACA
* * * * *
29521 TCATCTAACCAAATCTCAGCAACATTGGATCTAAAAATTTGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
* * *
29586 TTCGATTTAA-TAGAAATTAATTTAGAAAAA-ATAAAATATACGATATTAAAAGCGTAAAAAGCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA-A-ACGATATTAAAAGCGTGAAAAGCC
* * * * *
29649 CTCCAATCTTTTTGACGTTGAATTGTATTTTATTATGAGTATTTTAGGCAAAAATTGAGGAGAAA
129 CT-CAATCTTTTTGGCGTTGAATTATA-TATATTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
** *
29714 TCTTTCGTATCAATTTTTGTAAAATTTTAGTCC-AAATCGTGTACTAACAAACCATCAC-GATTT
192 T-TTTCGGGTCAATTTTTGCAAAATTTTAG-CCGAAATCGTGTACT----AACCATCACAG-TTT
** ** * * * *
29777 TTGGCTAAAAACGTATTTCGGGG-ACTTGGCTCAATTTTGCATGATTTTTGGCTCCTAGACTACT
250 TTGGCTAAAAACGCGTTTCGGGGCAC-CAGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
29841 T-AAATTATCTATAT
314 TGAAA-TATCTATAT
* * ** *
29855 TCATCTAATCAAATCTCACCCACATTAGATTTAAGGATTTGTTTTTACGACCATCTGAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
* * * * * *
29920 TTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGGAAAAC-AGTATTGGAAA-CGTCAAAAG
66 TTCGATTTAATTAGAAATTAA-TT-CAGAAAAATATGAAAAACGA-TATT-AAAAGCGTGAAAAG
* * * * * *
29983 CCCTTCAATCTTTTTGGCATTGAGTTATATGTTTTTAATGAGTACTTTAGCCAAAATTTGAGGAA
127 CCC-TCAATCTTTTTGGCGTTGAATTATAT-ATATT-ATGAGTATTTTAGCCAAAAATTGAGGAA
* * * *
30048 ATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAATTTTTG
189 AAAT-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTG
** * * *
30113 AATAAAAAAGCG-TTCTGGGGCCCCTA-CTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTG
253 GCTAAAAACGCGTTTC-GGGGCACC-AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG
*
30176 AGATATCTATAT
316 AAATATCTATAT
* * * * * * *
30188 TCATCTAATCAAATATCAACCACATTGGATTTAAAAATATGATTTTACAAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
* *
30253 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGGAAAACGATATTAGAAA-CGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGCCC
* *** *
30317 TCAAATCTTTTTGCCGCCAAATTATATATATTATGAGTATTTTATCCAAAAATTGAGGAAAAAAT
130 TC-AATCTTTTTGGCGTTGAATTATATATATTATGAGTATTTTAGCCAAAAATTGAGG-AAAAAT
* * * * * ** *
30382 TTTAGGGTCATTTTTTGTAAAATTTTATCCAAAATCGTGTACTAACCATCATGGTTTTTGGTTAA
193 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAA
* * * * * * *
30447 AAACGTGTTTCGGGGCACCAGTTCAGTTTTACATGATTTTTGGCGTC-GGCATTCCTTGATATAT
258 AAACGCGTTTCGGGGCACCAGCTCAGTTTTGCATGATTTTTGGCGCCAAG-ACTCCTTGAAATAT
30511 CTATAT
322 CTATAT
* * * * * *
30517 TCATCTAATAAAATCTTAGCCACATTGCATTT-AAGATTT-TTTTTACGAGCATCCGAAT-TATG
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCT-TA
* * * * * *
30579 TTTCGATTTAATTAGAAATTAATTCAAAAAAAATATTAAAAACAATATTAAAAGTGTCAAAAACC
65 TTTCGATTTAATTAGAAATTAATTC-AGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* * * *
30644 CTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGT-GACTAAAAATTGAGCAAA
129 C-TCAATCTTTTTGGCGTTGAATTATAT-A-TATTATGAGTATTTTAG-CCAAAAATTGAGGAAA
* * * * * *
30708 TAACTTTCGAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAATCAT-ATTACGTTTTT
190 -AATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA-CA-GTTTTT
* * * *
30772 GGCTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
252 GGCTAAAAACGCGTTTCGGGGCACCAGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
*
30837 GATAT-TCATAT
317 AATATCT-ATAT
** * *
30848 TCATCTAATCAAATCTCAGTTACATTGGATTTAAGAATATGTTTTTACGAGCATCTGAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
* * *
30913 TTCGATTTAATTAGAAATTAATTAAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCT
* * * *
30978 CCAATCTTTTTGACATTAAATTATATATATATGACGAGTA-TTTATGCCAAAAATTGATGGAAAA
131 -CAATCTTTTTGGCGTTGAATTATATATAT-T-ATGAGTATTTTA-GCCAAAAATTGA-GGAAAA
* ***
31042 ATTTTCGGGTCATTTTTTGCAAAATTTTAAATGAAATCGTGTACTAACCATCACAGTTTTTGGCT
191 ATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
* * *
31107 AAAATCGCGTTTC-GGG-ACCCGTCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
256 AAAAACGCGTTTCGGGGCACCAG-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
31170 ATCTATAT
320 ATCTATAT
* * * * * * * * *
31178 TCATGTAATAAAATCTTAGCCACATTGCATTT-AAGATTTTTTTTTACGAGCATCCGAATCATGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
* * *
31242 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACAATATTAAAAGCGTCAAAACCCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCC-
** * * * * *
31307 TCAATCTTTTTTTCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAATTGAGCAAATAA
130 TCAATCTTTTTGGCGTTGAATTATAT-A-TATTATGAGTATTTTAGCCAAAAATTGAGGAAA-AA
* * * * * * ** *
31372 CTTTCGAGTCAATTTTTGCAAAGTTCTAGCCGAAATCGTGTAATAATCATCATGGTTTTTGACTA
192 TTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTA
* * * * ** * *
31437 AAACCGCGTTCCGAGG-TCTTGCCTAAGTTTTGCATGATTTTTGGCGCCAAGACT-CTTAGAGAT
257 AAAACGCGTTTCGGGGCACCAG-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-GAAAT
*
31500 ATCCATAT
320 ATCTATAT
** * * *
31508 TCATCTAATCAAATCTCAGGTACATTGGATTTAAGAATTTGTTTTTACGAGCTTCTAAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
*
31573 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCT
* * * *
31638 CCATTCTTTTTGGCGTTAAATTTTATATATATATATATTGAGTA-CTTATGCGAAAAATTGATGG
131 -CAATCTTTTTGGCGTTGAA---T-TATATATAT-TA-TGAGTATTTTA-GCCAAAAATTGA-GG
* * * *
31702 AAAAATTTTGCGAGTCACTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCACCACAGTTTT
187 AAAAATTTT-CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTT
* ** * * * * *
31767 TGGCTAAAAACGCATTTCGGAAC-CCTATCTTAGTTTTGCATAATTTTTGGCACCGAGACTCCTT
251 TGGCTAAAAACGCGTTTCGGGGCACC-AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
31831 GAAATATCTATAT
315 GAAATATCTATAT
* * * **
31844 TCATCTAATAAAATCTCAGTCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
* *
31909 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAGAGTCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCT
* * *
31974 CTAATCTATTTGGCGTTTGTTTAATTATATATACTCTATGAGTA-TTAAGGCTAAAAATTGAGGA
131 C-AATCTTTTTGGCG-TTG---AATTATATATA-T-TATGAGTATTTTA-GCCAAAAATTGAGGA
* * * ** *****
32038 GAAATATTTCGGGTCAATTTTTGCAAAGTTTTAGCCGAAATCGTGTACCATCACGGTTTTTTTTT
188 AAAAT-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-C-TAAC-CATCACAGTT
* * * * * * * * *
32103 TTTTGCTAAAAACGCG-TTCTGGGGCCCCGGGTCAATTTTGCATGATTTTTGGTGGCTACACTCC
249 TTTGGCTAAAAACGCGTTTC-GGGGCACCAGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
*
32167 TTGAAATTTCTATAT
313 TTGAAATATCTATAT
* * * ** * * *
32182 TCATCTAACCAAATTTTAGCCACATTGGATTTAAGGATTTATTTTTACGAGCAT-TGGAATCCTG
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCT-GAATCTTA
* * * *
32246 TTTCAATTTAATTAGAAATTAATT--G--AAA-A--AAACA-GGTA-TAAGAAGCGTGAGAA-CC
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAA-AAGCGTGAAAAGCC
* * * * * * * ** *
32301 TCTTCAATCTTTTTTGGCATTGAATTATATATTTTTTATAAGTATTGT-GGC-TAATTTTTGCAA
129 -C-TCAATC-TTTTTGGCGTTGAATTATATA--TATTATGAGTATTTTAGCCAAAAATTGAGGAA
* * **
32364 AAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCTAAAT--TGT-GT-ACCATCATGGTTTTTT
189 AAAT-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTT
* * * * *
32425 AGCTAAAAACGTGTTCCGGGGC-CCTA-CGTCAGTTTTGCATGATTTTTGACGACAAGACTCCTT
252 GGCTAAAAACGCGTTTCGGGGCACC-AGC-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCC--
* *
32488 AAAATATATATATATATATATAT
313 ----T-T-GA-A-ATATCTATAT
* * ** * ** * * *
32511 TCATCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTTCGAGTTTATAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
* * * * * *
32576 TTCGATTTAATCAGAAATTAATTTTGAAATAAAATAAGAAAAACGATATTAGAAGCATGAAAAGG
66 TTCGATTTAATTAGAAATTAA--TTCAGA-AAAATATGAAAAACGATATTAAAAGCGTGAAAA--
** * * * * * *
32641 GCTTTCAAAT-TTTTTGGCGTTGAATTCTATATTTTTTATGAGTATTCTCGCTAGAAATTGA-GA
126 GCCCTC-AATCTTTTTGGCGTTGAA-T-TATATATATTATGAGTATTTTAGCCAAAAATTGAGGA
**
32704 AAAACTCTTTCGGCTTCGGCTCAATTTTTGCAAAA-TTTAGCCGAAATTTTGTACTAACCATCAC
188 AAAA-T-TTTC-G----GG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
** * * * * * * * *
32768 -GATTTTCAGCTAAAAACACATTCCGGGGC-CCGGATCAATTTTGCATGATTTTTGGTGTCAAGA
245 AG-TTTTTGGCTAAAAACGCGTTTCGGGGCACCAGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
** *
32831 CTTTTTGAAATATCCATAT
309 CTCCTTGAAATATCTATAT
* * * * ** * * *
32850 TCATCTAACCAAATCTTAGCTACATTAGATTTAAGGATTTGTTTATACGAGCATATGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
* * * * * * * *
32915 TTCTATTTAATTATAAATTAATTCGGAAAAAAAAAATAGGAGAAACAATATTAGAAGCGTTAAAA
66 TTCGATTTAATTAGAAATTAATTC-----AGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
*** * *
32980 GCCCTTCAATC-TTTTGATATCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAAGTTGAGG
126 GCCC-TCAATCTTTTTGGCGTTGAATTATATA--TATTATGAGTATTTTAGCCAAAAA-TTGAGG
* * * *
33044 AAATATCTTTCGGGTAAATTTTTGTAAAATTTTAGCCGAAATCGTG----------CACGGTTTT
187 AAAAAT-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTT
* * * * * *
33099 TGGCTAAAAACGCGTTACAGGGTCA-CGGCTCTGTTTTGCATGATTTTTGGTGCCGAGACTCCTT
251 TGGCTAAAAACGCGTTTC-GGGGCACCAGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
*
33163 GAAATATCTTTAT
315 GAAATATCTATAT
* * * * *
33176 TCATCTAATCAAATCTCAGCTACATTGGATTTAAAGATTTGTTTTTATGTGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
* *
33241 TTCGATTTAATTAGAAATTAATTCAGAAAAAAATATGAAAAATGATATTAAAA--G-GAAAAGTC
66 TTCGATTTAATTAGAAATTAATTCAG--AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* * *
33303 TTCTAATCTTTTTTGCGTTGAATTTTATATATT
129 CTC-AATCTTTTTGGCGTTGAATTATATATATT
33336 TTTGATTATT
Statistics
Matches: 2807, Mismatches: 521, Indels: 321
0.77 0.14 0.09
Matches are distributed among these distances:
318 4 0.00
319 55 0.02
320 13 0.00
321 16 0.01
323 23 0.01
325 65 0.02
326 130 0.05
327 62 0.02
328 62 0.02
329 439 0.16
330 256 0.09
331 286 0.10
332 125 0.04
333 193 0.07
334 90 0.03
335 97 0.03
336 318 0.11
337 98 0.03
338 138 0.05
339 123 0.04
340 53 0.02
341 45 0.02
342 21 0.01
343 3 0.00
347 13 0.00
348 15 0.01
349 30 0.01
350 27 0.01
351 7 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (327 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGCATCTGAATCTTAT
TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCT
CAATCTTTTTGGCGTTGAATTATATATATTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTT
CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA
CGCGTTTCGGGGCACCAGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTAT
AT
Found at i:30850 original size:660 final size:661
Alignment explanation
Indices: 29521--33338 Score: 3516
Period size: 660 Copynumber: 5.7 Consensus size: 661
29511 ATACTTTACA
* * * *
29521 TCATCTAACCAAATCTCAGCAACATTGGATCTAAAAATTTGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAACCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
29586 TTCGATTTAA-TAGAAATTAATTTAGAAAAA-ATAAAATATACGATATTAAAAGCGTAAAAAGCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA-A-ACGATATTAAAAGCGTGAAAAGTC
* * * * * *
29649 CTCCAATCTTTTTGACGTTGAATTGTATTTTATTATGAGTATTTTAGGCAAAAATTGAGGAGAAA
129 CTCCAATCTTTTTGACATTAAATTATA-TATATTATGAGTATTTTAGCCAAAAATTGAGGAAAAA
** * *
29714 TCTTTCGTATCAATTTTTGTAAAATTTTAGTCC-AAATCGTGTACTAACAAACCATCACGATTTT
193 TCTTTCGGGTCAATTTTTGCAAAATTTTAG-CCGAAATCGTGTACT----AACCATCACGGTTTT
** ** * * * * *
29778 TGGCTAAAAACGTATTTCGGGG-ACTTGGCTCAATTTTGCATGATTTTTGGCTCCTAGACTACTT
253 TGGCTAAAAACGCGTTTCGGGGCAC-CAGTTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
* *
29842 -AAATTATCTATATTCATCTAATCAAATCTCACCCACATTAG-ATTTAAGGATTTGTTTTTACGA
317 GAAA-TATCTATATTCATCTAATAAAATCTCAGCCACATT-GCATTTAAGGATTTGTTTTTACGA
* * ** * * *
29905 CCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTGGAAAAAAATAGGGAAAACAGTATTG
380 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCAAAAAAAATATGAAAAACAATATT-
* * * *
29970 GAAA-CGTCAAAAGCCCTTC-AATCTTTTTGGCATTGAGTTATAT-GTTTTTAATGAGTACTT-T
443 AAAAGCGTCAAAAGCCCTTCTAATCTTTTTGGCGTTGAATTATATAATTTTT-ATGAGTA-TTGT
* * * * * *
30031 -AGCCAAAATTTGAGGAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAA
506 GA-CTAAAAATTGAGCAAATAACTTTCGGGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAA
* * * ** * * ** * *
30095 TAACCATCACAATTTTTGAATAAAAAAGCGTTCTGGGGCCCCTACTCAGTTTTGTATGATTTTTG
570 TAACTATTAC-GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGCATGATTTTTG
30160 GCGCCAAGACTCCTTGAGATA-TCTATAT
634 GCGCCAAGACTCCTTGAGATATTC-ATAT
* * * * * * * * *
30188 TCATCTAATCAAATATCAACCACATTGGATTTAAAAATATGATTTTACAAGCATCTAAATCTTGT
1 TCATCTAACCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
*
30253 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGGAAAACGATATTAGAAA-CGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGTCC
* * *** *
30317 TCAAATCTTTTTGCCGCCAAATTATATATATTATGAGTATTTTATCCAAAAATTGAGGAAAAAAT
130 TCCAATCTTTTTGACATTAAATTATATATATTATGAGTATTTTAGCCAAAAATTGAGG-AAAAAT
* * * * * * *
30382 -TTTAGGGTCATTTTTTGTAAAATTTTATCCAAAATCGTGTACTAACCATCATGGTTTTTGGTTA
194 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTA
* * * * * *
30446 AAAACGTGTTTCGGGGCACCAGTTCAGTTTTACATGATTTTTGGCGTC-GGCATTCCTTGATATA
259 AAAACGCGTTTCGGGGCACCAGTTCAGTTTTGCATGATTTTTGGCGCCAAG-ACTCCTTGAAATA
* *
30510 TCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAA-GATTT-TTTTTACGAGCATCCGA
323 TCTATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGA
* *
30573 AT-TATGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATTAAAAACAATATTAAAAGTGTC
388 ATCT-TGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAAAAACAATATTAAAAGCGTC
*
30637 AAAAACCCTTC-AATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGACTAAAAATT
452 AAAAGCCCTTCTAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGACTAAAAATT
*
30701 GAGCAAATAACTTTCGAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAATCATATTAC
517 GAGCAAATAACTTTCGGGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAA-C-TATTAC
30766 GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACT
580 GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACT
30831 CCTTGAGATATTCATAT
645 CCTTGAGATATTCATAT
* * * *
30848 TCATCTAATCAAATCTCAGTTACATTGGATTTAAGAATATGTTTTTACGAGCATCTGAATCTTAT
1 TCATCTAACCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* *
30913 TTCGATTTAATTAGAAATTAATTAAGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
*
30978 CCAATCTTTTTGACATTAAATTATATATATATGACGAGTA-TTTATGCCAAAAATTGATGGAAAA
131 CCAATCTTTTTGACATTAAATTATATATAT-T-ATGAGTATTTTA-GCCAAAAATTGA-GGAAAA
* *** *
31042 AT-TTTCGGGTCATTTTTTGCAAAATTTTAAATGAAATCGTGTACTAACCATCACAGTTTTTGGC
192 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC
* * *
31106 TAAAATCGCGTTTC-GGG-ACCCGTCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
257 TAAAAACGCGTTTCGGGGCACCAGT-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
* * * *
31169 TATCTATATTCATGTAATAAAATCTTAGCCACATTGCATTTAA-GATTTTTTTTTACGAGCATCC
321 TATCTATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCT
* *
31233 GAATCATGTTTCGATTTAATTAGAAATTAATTC-AGAAAAATATGAAAAACAATATTAAAAGCGT
386 GAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAAAAACAATATTAAAAGCGT
* ** *
31297 CAAAACCCCTTC-AATCTTTTTTTCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAAT
451 CAAAAGCCCTTCTAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGACTAAAAAT
* * *
31361 TGAGCAAATAACTTTCGAGTCAATTTTTGCAAAGTTCTAGCCGAAATCGTGTAATAA-TCATCAT
516 TGAGCAAATAACTTTCGGGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAACT-ATTA-
* * * * * ** *
31425 GGTTTTTGACTAAAACCGCGTTCCGAGGTCTTGCCTAAGTTTTGCATGATTTTTGGCGCCAAGAC
579 CGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGCCAAGAC
*
31490 T-CTTAGAGATATCCATAT
644 TCCTT-GAGATATTCATAT
* * * * *
31508 TCATCTAATCAAATCTCAGGTACATTGGATTTAAGAATTTGTTTTTACGAGCTTCTAAATCTTAT
1 TCATCTAACCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
31573 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
66 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * * *
31638 CCATTCTTTTTGGCGTTAAATTTTATATATATATATATTGAGTA-CTTATGCGAAAAATTGATGG
131 CCAATCTTTTTGACATTAAA---T-TATATATAT-TA-TGAGTATTTTA-GCCAAAAATTGA-GG
* * * * *
31702 AAAAAT-TTTGCGAGTCACTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCACCACAGTTT
188 AAAAATCTTT-CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
* ** * * * *
31766 TTGGCTAAAAACGCATTTCGGAAC-CCTA-TCTTAGTTTTGCATAATTTTTGGCACCGAGACTCC
252 TTGGCTAAAAACGCGTTTCGGGGCACC-AGT-TCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* *
31829 TTGAAATATCTATATTCATCTAATAAAATCTCAGTCACATTGAATTTAAGGATTTGTTTTTACGA
315 TTGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGA
* * *
31894 GCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTC-AGAAAAATATGAAAAACGATATTAA
380 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAAAAACAATATTAA
* * * * * * *
31958 AAGCGTGAAGAGTCC-TCTAATCTATTTGGCGTTTGTTTAATTATAT-ATACTCTATGAGTATTA
445 AAGCGTCAAAAGCCCTTCTAATCTTTTTGGCG-TTG---AATTATATAAT-TTTTATGAGTATTG
* * * * *
32021 AGGCTAAAAATTGAGGAGAA-ATA-TTTCGGGTCAATTTTTGCAAAGTTTTAGCCGAAATCGTGT
505 TGACTAAAAATTGAGCA-AATA-ACTTTCGGGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGT
* * *** * * *
32084 ACCATCACGGTTTTTTTTTTTTTGCTAAAAACGCGTTCTGGGGCCCCGGGTCAA-TTTTGCATGA
568 A--ATAAC--TATTACGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCT-AAGTTTTGCATGA
* * * * *
32148 TTTTTGGTGGCTACACTCCTTGAAAT-TTCTATAT
628 TTTTTGGCGCCAAGACTCCTTGAGATATTC-ATAT
* * * * * *
32182 TCATCTAACCAAATTTTAGCCACATTGGATTTAAGGATTTATTTTTACGAGCAT-TGGAATCCTG
1 TCATCTAACCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCT-GAATCTTG
* * * *
32246 TTTCAATTTAATTAGAAATTAATT--G--AAA-A--AAACA-GGTA-TAAGAAGCGTGAGAA--C
65 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAA-AAGCGTGAAAAGTC
* * * * * * * * ** *
32300 CTCTTCAATCTTTTTTGGCATTGAATTATATATTTTTTATAAGTATTGT-GGC-TAATTTTTGCA
129 CTC--CAATC-TTTTTGACATTAAATTATATA--TATTATGAGTATTTTAGCCAAAAATTGAGGA
* * * *
32363 AAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCTAAAT--TGT-GT-ACCATCATGGTTTTT
189 AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTT
* * * * *
32424 TAGCTAAAAACGTGTTCCGGGGC-CCTACG-TCAGTTTTGCATGATTTTTGACGACAAGACTCCT
253 TGGCTAAAAACGCGTTTCGGGGCACC-A-GTTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-
* * ** *
32487 TAAAATATATATATATATATATATTCATCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTG
315 -----T-T-GA-A-ATATCTATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGGATTTG
* ** * * * * * *
32552 TTTTTTCGAGTTTATAAATCTTGTTTCGATTTAATCAGAAATTAATTTTGAAATAAAATAAGAAA
371 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA--TTCAAAAAAAATATGAAA
* * * * * * * * *
32617 AACGATATTAGAAGCATGAAAAGGGCTTTCAAAT-TTTTTGGCGTTGAATTCTATATTTTTTATG
434 AACAATATTAAAAGCGTCAAAA-GCCCTTCTAATCTTTTTGGCGTTGAATTATATAATTTTTATG
* *
32681 AGTATTCTCG-CTAGAAATTGAG-AAA-AACTCTTTCGGCTTCGGCTCAATTTTTGCAAAATT-T
498 AGTATTGT-GACTAAAAATTGAGCAAATAA--CTTTC-G----GG-TCAATTTTTGCAAAATTCT
** * * * ** * * *
32742 AGCCGAAATTTTGTACTAACCATCACGATTTTCAGCTAAAAACACATTCCGGGG-CCCGGATCAA
554 AGCCGAAATCGTGTAATAACTATTACG-TTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCT-AA
* * ** * *
32806 -TTTTGCATGATTTTTGGTGTCAAGACTTTTTGAAATATCCATAT
617 GTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAGATATTCATAT
* * * * *
32850 TCATCTAACCAAATCTTAGCTACATTAGATTTAAGGATTTGTTTATACGAGCATATGAATCTTGT
1 TCATCTAACCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * * *
32915 TTCTATTTAATTATAAATTAATTCGGAAAAAAAAAATAGGAGAAACAATATTAGAAGCGTTAAAA
66 TTCGATTTAATTAGAAATTAATTC-----AGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
* * * ** *
32980 GCCCTTCAATC-TTTTGATATCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAAGTTGAGG
126 GTCCTCCAATCTTTTTGACATTAAATTATATA--TATTATGAGTATTTTAGCCAAAAA-TTGAGG
* * *
33044 AAATATCTTTCGGGTAAATTTTTGTAAAATTTTAGCCGAAATCGTG----------CACGGTTTT
188 AAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
* * * * * * *
33099 TGGCTAAAAACGCGTTACAGGGTCA-CGGCTCTGTTTTGCATGATTTTTGGTGCCGAGACTCCTT
253 TGGCTAAAAACGCGTTTC-GGGGCACCAGTTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
* * * * * * *
33163 GAAATATCTTTATTCATCTAATCAAATCTCAGCTACATTGGATTTAAAGATTTGTTTTTATGTGC
317 GAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGC
**
33228 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATATGAAAAATGATATTAAA
382 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA-AAAAAAATATGAAAAACAATATTAAA
* * *
33293 AG-G--AAAAG-TCTTCTAATCTTTTTTGCGTTGAATTTTATATATTTTT
446 AGCGTCAAAAGCCCTTCTAATCTTTTTGGCGTTGAATTATATA-ATTTTT
33339 GATTATTTTT
Statistics
Matches: 2647, Mismatches: 381, Indels: 252
0.81 0.12 0.08
Matches are distributed among these distances:
656 7 0.00
657 53 0.02
658 9 0.00
659 138 0.05
660 528 0.20
661 259 0.10
662 234 0.09
663 23 0.01
664 77 0.03
665 157 0.06
666 166 0.06
667 340 0.13
668 153 0.06
669 32 0.01
670 41 0.02
671 84 0.03
672 25 0.01
673 22 0.01
674 130 0.05
675 53 0.02
676 10 0.00
677 3 0.00
678 1 0.00
679 32 0.01
680 5 0.00
681 18 0.01
682 42 0.02
683 3 0.00
684 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (661 bp):
TCATCTAACCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
CCAATCTTTTTGACATTAAATTATATATATTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCT
TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAA
AACGCGTTTCGGGGCACCAGTTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCT
ATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATC
TTGTTTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAAAAACAATATTAAAAGCGTCAAAA
GCCCTTCTAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGACTAAAAATTGAGC
AAATAACTTTCGGGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAACTATTACGTTTTT
GGCTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
GATATTCATAT
Found at i:33792 original size:2 final size:2
Alignment explanation
Indices: 33785--33823 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
33775 GGAGCACAAG
*
33785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33824 TATTTGAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:34205 original size:216 final size:215
Alignment explanation
Indices: 33832--34262 Score: 817
Period size: 216 Copynumber: 2.0 Consensus size: 215
33822 ATTATTTGAA
33832 ACACCCAATGAAATTACTAAATGCTCCTTTTGAGGATCGATGAGGAGGCTTGGTTTAAACGTTTT
1 ACACCCAATGAAATTACTAAATGCTCCTTTTGAGGATCGATGAGGAGGCTTGGTTTAAACGTTTT
*
33897 TTGTCCTTTTTGTTTTTTCTCACTTGGTTAATTACCAAAAAATACTATTAATATTAACATTATTA
66 TTGTCCTTTTTGTCTTTTCTCACTTGGTTAATTACCAAAAAATACTATTAATATTAACATTATTA
*
33962 CTTCAATGAAGTTACTATTTGATCCCATATTTGGGTTAATGAGGGGCTAGATTATTAAATATTTT
131 CTTCAATGAAGTTACTATTTGATCCCATATTTGGGTTAATAAGGGGCTAGATTATTAAATATTTT
34027 AGTTTTTAGTCTTTTTCCAT
196 AGTTTTTAGTCTTTTTCCAT
34047 ACACCCAATGAAATTACTAAATGCTCCTTTTGAGGATCGATGAGGAGGCTTGGTTTAAACGTTTT
1 ACACCCAATGAAATTACTAAATGCTCCTTTTGAGGATCGATGAGGAGGCTTGGTTTAAACGTTTT
* *
34112 TTGTCCTTTTTTGTCTTTTCTCACTTGGTTAATTACCAAAAAGTACTATTAATGTTAACATTATT
66 TTGTCC-TTTTTGTCTTTTCTCACTTGGTTAATTACCAAAAAATACTATTAATATTAACATTATT
34177 ACTTCAATGAAGTTACTATTTGATCCCATATTTGGGTTAATAAGGGGCTAGATTATTAAATATTT
130 ACTTCAATGAAGTTACTATTTGATCCCATATTTGGGTTAATAAGGGGCTAGATTATTAAATATTT
34242 TAGTTTTTAGTCTTTTTCCAT
195 TAGTTTTTAGTCTTTTTCCAT
34263 TGACCAAATC
Statistics
Matches: 211, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
215 71 0.34
216 140 0.66
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (215 bp):
ACACCCAATGAAATTACTAAATGCTCCTTTTGAGGATCGATGAGGAGGCTTGGTTTAAACGTTTT
TTGTCCTTTTTGTCTTTTCTCACTTGGTTAATTACCAAAAAATACTATTAATATTAACATTATTA
CTTCAATGAAGTTACTATTTGATCCCATATTTGGGTTAATAAGGGGCTAGATTATTAAATATTTT
AGTTTTTAGTCTTTTTCCAT
Found at i:35673 original size:16 final size:16
Alignment explanation
Indices: 35652--35685 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
35642 TTCTTTAGGG
35652 AATAATTTTTAATTTT
1 AATAATTTTTAATTTT
35668 AATAATTTTTAATTTT
1 AATAATTTTTAATTTT
35684 AA
1 AA
35686 ATACAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATAATTTTTAATTTT
Found at i:39300 original size:19 final size:19
Alignment explanation
Indices: 39276--39326 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
39266 AAATTTTATG
*
39276 TATTTTTACCTTTATCTTC
1 TATTTTTACCCTTATCTTC
39295 TATTTTTACCCTTATCTTC
1 TATTTTTACCCTTATCTTC
39314 TATTTTTACCCTT
1 TATTTTTACCCTT
39327 GTTCTTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTTACCCTTATCTTC
Found at i:39332 original size:20 final size:19
Alignment explanation
Indices: 39276--39332 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
39266 AAATTTTATG
39276 TATTTTTA-CCTTTATCTTC
1 TATTTTTACCCTTT-TCTTC
*
39295 TATTTTTACCCTTATCTTC
1 TATTTTTACCCTTTTCTTC
39314 TATTTTTACCCTTGTTCTT
1 TATTTTTACCCTT-TTCTT
39333 TTTCCCCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 26 0.76
20 8 0.24
ACGTcount: A:0.14, C:0.23, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTTTACCCTTTTCTTC
Found at i:40345 original size:30 final size:29
Alignment explanation
Indices: 40301--40358 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
40291 CCTTCAATTT
40301 AAAAAAGGCAATTGCGTCAAATCAAAAAA
1 AAAAAAGGCAATTGCGTCAAATCAAAAAA
*
40330 AAAAAATGGCGATTGCGTCAAATCAAAAA
1 AAAAAA-GGCAATTGCGTCAAATCAAAAA
40359 TATCTTCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (29 bp):
AAAAAAGGCAATTGCGTCAAATCAAAAAA
Found at i:40438 original size:92 final size:93
Alignment explanation
Indices: 40310--40486 Score: 304
Period size: 92 Copynumber: 1.9 Consensus size: 93
40300 TAAAAAAGGC
40310 AATTGCGTCAAATCAAAAAAAAAAAATGGCGATTGCGTCAAATCAAAAATATCTTCTATAAATAA
1 AATTGCGTCAAATCAAAAAAAAAAAATGGCGATTGCGTCAAATCAAAAATATCTTCTATAAATAA
* *
40375 AAGGTCAACTATAACTTAATTTAATAAA
66 AAAGTCAACTATAACATAATTTAATAAA
*
40403 AATTGCGTCTACATC-AAAAAAAAAAA-GGCGATTGCGTCAAATCAAAAATATCTTCTATAAATA
1 AATTGCGTC-AAATCAAAAAAAAAAAATGGCGATTGCGTCAAATCAAAAATATCTTCTATAAATA
40466 AAAAGTCAACTATAACATAAT
65 AAAAGTCAACTATAACATAAT
40487 CGGTACCTAT
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
92 56 0.70
93 20 0.25
94 4 0.05
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (93 bp):
AATTGCGTCAAATCAAAAAAAAAAAATGGCGATTGCGTCAAATCAAAAATATCTTCTATAAATAA
AAAGTCAACTATAACATAATTTAATAAA
Found at i:45999 original size:27 final size:29
Alignment explanation
Indices: 45946--46000 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
45936 CTATATTGAC
* *
45946 ATTATTAAAATATATTTTAATTATGCCATT
1 ATTATTAAAATATA-TTAAAATATGCCATT
45976 ATTATTAAAATATA-TAAAAT-TGCCA
1 ATTATTAAAATATATTAAAATATGCCA
46001 ATATGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 4 0.17
30 14 0.61
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (29 bp):
ATTATTAAAATATATTAAAATATGCCATT
Found at i:46010 original size:46 final size:43
Alignment explanation
Indices: 45954--46043 Score: 135
Period size: 43 Copynumber: 2.0 Consensus size: 43
45944 ACATTATTAA
*
45954 AATATATTTTAATTATGCCATTATTATTAAAATATATAAAATTGCC
1 AATATATTTTAATTATG---TCATTATTAAAATATATAAAATTGCC
*
46000 AATATGTTTTAATTATGTCATTATTAAAATATATAAAATTGCC
1 AATATATTTTAATTATGTCATTATTAAAATATATAAAATTGCC
46043 A
1 A
46044 TTATTAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 26 0.62
46 16 0.38
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (43 bp):
AATATATTTTAATTATGTCATTATTAAAATATATAAAATTGCC
Found at i:46878 original size:22 final size:22
Alignment explanation
Indices: 46853--46900 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
46843 CTATGGTATC
*
46853 AAAAATTT-ATAGGGAGATTA-
1 AAAAATTTCATAGAGAGATTAT
*
46873 ATAAAATTTCATAGAGAGGTTAT
1 A-AAAATTTCATAGAGAGATTAT
46896 AAAAA
1 AAAAA
46901 AAATCATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 7 0.30
22 14 0.61
23 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.17, T:0.29
Consensus pattern (22 bp):
AAAAATTTCATAGAGAGATTAT
Found at i:46880 original size:21 final size:21
Alignment explanation
Indices: 46854--46899 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
46844 TATGGTATCA
*
46854 AAAATTT-ATAGGGAGATTAAT
1 AAAATTTCATAGAGAGATT-AT
*
46875 AAAATTTCATAGAGAGGTTAT
1 AAAATTTCATAGAGAGATTAT
46896 AAAA
1 AAAA
46900 AAAATCATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.30
Consensus pattern (21 bp):
AAAATTTCATAGAGAGATTAT
Found at i:50280 original size:17 final size:18
Alignment explanation
Indices: 50260--50293 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50250 GTAAAAAAAC
50260 TGACTAAAC-AAACAAAT
1 TGACTAAACAAAACAAAT
*
50277 TGACTCAACAAAACAAA
1 TGACTAAACAAAACAAA
50294 CTAACGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.21, G:0.06, T:0.15
Consensus pattern (18 bp):
TGACTAAACAAAACAAAT
Found at i:51009 original size:15 final size:14
Alignment explanation
Indices: 50986--51015 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
50976 ATAAAAATTA
50986 AATATTTTTATTTT
1 AATATTTTTATTTT
51000 AATATATTTTATTTT
1 AATAT-TTTTATTTT
51015 A
1 A
51016 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:52533 original size:251 final size:253
Alignment explanation
Indices: 52069--52572 Score: 843
Period size: 250 Copynumber: 2.0 Consensus size: 253
52059 CCCAGAATTG
* *
52069 GGTAAAAGTACCCGGGAGGTCCCTATACTATACGAAATATTGATTTTGGTCCATGTACTTGTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTATACTATACAAAATATTGATTTTGATCCATGTACTTGTTTT
*
52134 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
66 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCAAGGTCCCTCACGTTAGCATGCCGT
* * *
52199 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTAACGTGGCAGATGAC
131 GACAAACCCGTCAAATATGCTGACGTGGCACTAACAACGTCTTTTTTGCTAACGCGGCAGATGAC
52264 ACGTGGAATAAAAATTAAAT-TTTTTT-AATATATTTTATTTTATTGAAATTTATTTT
196 ACGTGGAATAAAAATTAAATATTTTTTAAATATATTTTATTTTATTGAAATTTATTTT
* * * *
52320 GGTAAAAGTATCCGGGAGGTCCCTGTACTATACAAAATGTTGATTTTGATCCCTGTACTT-TTTT
1 GGTAAAAGTACCCGGGAGGTCCCTATACTATACAAAATATTGATTTTGATCCATGTACTTGTTTT
*
52384 TTCTACAAATTTGTCCCTCTACTATCAGAACCTATCACCCAAGGTCCCTCACGTTAGCATGCCGT
66 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCAAGGTCCCTCACGTTAGCATGCCGT
* *
52449 GACAAACCCGTCAAATATGCTGACGTGGCACTAACAACGTCTTCTTTTGCTGACGCGGCAGGTGA
131 GACAAACCCGTCAAATATGCTGACGTGGCACTAACAACGTCTT-TTTTGCTAACGCGGCAGATGA
* *
52514 CACGTGGAATAAAAATTAAATATTTTTTAAATATATTTTATTTTATTGAATTTTTTTTT
195 CACGTGGAATAAAAATTAAATATTTTTTAAATATATTTTATTTTATTGAAATTTATTTT
52573 TTAAAAAAAA
Statistics
Matches: 235, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
250 108 0.46
251 93 0.40
252 6 0.03
253 28 0.12
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (253 bp):
GGTAAAAGTACCCGGGAGGTCCCTATACTATACAAAATATTGATTTTGATCCATGTACTTGTTTT
TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCAAGGTCCCTCACGTTAGCATGCCGT
GACAAACCCGTCAAATATGCTGACGTGGCACTAACAACGTCTTTTTTGCTAACGCGGCAGATGAC
ACGTGGAATAAAAATTAAATATTTTTTAAATATATTTTATTTTATTGAAATTTATTTT
Found at i:53791 original size:15 final size:15
Alignment explanation
Indices: 53759--53788 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53749 TAAATTTCAA
53759 TAAAATAAAATATAT
1 TAAAATAAAATATAT
53774 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
53788 T
1 T
53789 TAATTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:71204 original size:19 final size:18
Alignment explanation
Indices: 71180--71221 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
71170 AAATGCAGTA
71180 ACTTTAATGCTGCACCCTC
1 ACTTTAAT-CTGCACCCTC
* *
71199 ACTTT-ATTTGCACCCTG
1 ACTTTAATCTGCACCCTC
71216 ACTTTA
1 ACTTTA
71222 TTTGCATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 13 0.65
18 2 0.10
19 5 0.25
ACGTcount: A:0.21, C:0.31, G:0.10, T:0.38
Consensus pattern (18 bp):
ACTTTAATCTGCACCCTC
Found at i:71210 original size:17 final size:17
Alignment explanation
Indices: 71190--71227 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
71180 ACTTTAATGC
71190 TGCACCCTCACTTTATT
1 TGCACCCTCACTTTATT
*
71207 TGCACCCTGACTTTATT
1 TGCACCCTCACTTTATT
71224 TGCA
1 TGCA
71228 TCAATAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.32, G:0.11, T:0.39
Consensus pattern (17 bp):
TGCACCCTCACTTTATT
Found at i:75229 original size:148 final size:150
Alignment explanation
Indices: 74987--75275 Score: 519
Period size: 148 Copynumber: 1.9 Consensus size: 150
74977 ATTTATATCA
* *
74987 CGCACCAAACATTTAATTGAAGCGTATTTAAAAGACAATATAAAATTCTAATTTCCTTAGTAAAT
1 CGCACCAAACATTTAATTGAAGCATATCTAAAAGACAATATAAAATTCTAATTTCCTTAGTAAAT
*
75052 ATATTACTATAAAATATAAATGATCTTGAATTACGATCATTGTAAA-TCATATCTAA-CAAAAAT
66 ATATTACTATAAAATATAAACGATCTTGAATTACGATCATTGTAAATTCATATCTAACCAAAAAT
*
75115 AAGCATGTACCTTCAACTCC
131 AAGCATATACCTTCAACTCC
*
75135 CGCACCAAACATTTAATTGAAGCATATCTAAAAGGCAATATAAAATTCTAATTTCCTTAGTAAAT
1 CGCACCAAACATTTAATTGAAGCATATCTAAAAGACAATATAAAATTCTAATTTCCTTAGTAAAT
75200 ATATTACTATAAAATATAAACGATCTTGAATTACGATCATTGTAAATTCATATCTAACCAAAAAT
66 ATATTACTATAAAATATAAACGATCTTGAATTACGATCATTGTAAATTCATATCTAACCAAAAAT
75265 AAGCATATACC
131 AAGCATATACC
75276 ACCAAAAAAT
Statistics
Matches: 134, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 107 0.80
149 10 0.07
150 17 0.13
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (150 bp):
CGCACCAAACATTTAATTGAAGCATATCTAAAAGACAATATAAAATTCTAATTTCCTTAGTAAAT
ATATTACTATAAAATATAAACGATCTTGAATTACGATCATTGTAAATTCATATCTAACCAAAAAT
AAGCATATACCTTCAACTCC
Found at i:75498 original size:34 final size:34
Alignment explanation
Indices: 75454--75520 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
75444 CCAGCATTTG
* *
75454 TTTTTGACATTCACAAGATGTTTTTAGCATTCAC
1 TTTTCGACATTCACAAGATGTTTTCAGCATTCAC
75488 TTTTCGACATTCACAAGATGTTTTCAGCATTCA
1 TTTTCGACATTCACAAGATGTTTTCAGCATTCA
75521 TAAAATTCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (34 bp):
TTTTCGACATTCACAAGATGTTTTCAGCATTCAC
Found at i:75518 original size:20 final size:20
Alignment explanation
Indices: 75461--75520 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
75451 TTGTTTTTGA
*
75461 CATTCACAAGATGTTTTTAG
1 CATTCACAAGATGTTTTCAG
75481 CATTCAC------TTTTC-G
1 CATTCACAAGATGTTTTCAG
75494 ACATTCACAAGATGTTTTCAG
1 -CATTCACAAGATGTTTTCAG
75515 CATTCA
1 CATTCA
75521 TAAAATTCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 16
0.65 0.02 0.33
Matches are distributed among these distances:
13 1 0.03
14 11 0.35
20 18 0.58
21 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (20 bp):
CATTCACAAGATGTTTTCAG
Found at i:87980 original size:112 final size:112
Alignment explanation
Indices: 87783--88006 Score: 376
Period size: 112 Copynumber: 2.0 Consensus size: 112
87773 AGACAATCTT
* * * *
87783 TAGCCAAAGTATAGCATGTATAAGAATCAACCGTACCATGTTTTGAGAAGTTTACAACAACGCCA
1 TAGCCAAAGTATAGCATGGATAAGAATCAACCATACCATGTTTTAAGAAGTGTACAACAACGCCA
87848 TGGTCGCTGCATCCAGCTCCACGATCAACGCCATAACATGTTGCATC
66 TGGTCGCTGCATCCAGCTCCACGATCAACGCCATAACATGTTGCATC
*
87895 TAGCCAAAGTATAGCATGGATGAGAATCAACCATACCATGTTTTAAGAAGTGTACAACAACGCCA
1 TAGCCAAAGTATAGCATGGATAAGAATCAACCATACCATGTTTTAAGAAGTGTACAACAACGCCA
* * *
87960 TGGTCGCTGCATCCAGCTCCACGATTAATGCCATACCATGTTGCATC
66 TGGTCGCTGCATCCAGCTCCACGATCAACGCCATAACATGTTGCATC
88007 CCTTGAGCTC
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 104 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (112 bp):
TAGCCAAAGTATAGCATGGATAAGAATCAACCATACCATGTTTTAAGAAGTGTACAACAACGCCA
TGGTCGCTGCATCCAGCTCCACGATCAACGCCATAACATGTTGCATC
Found at i:103916 original size:18 final size:18
Alignment explanation
Indices: 103893--103938 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
103883 TTAAGGCACT
103893 ATTATTTTACTTTGCTAG
1 ATTATTTTACTTTGCTAG
103911 ATTATTTTACTTTGCTAG
1 ATTATTTTACTTTGCTAG
103929 ATTATTTTAC
1 ATTATTTTAC
103939 ATGTTTTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.57
Consensus pattern (18 bp):
ATTATTTTACTTTGCTAG
Found at i:105483 original size:66 final size:65
Alignment explanation
Indices: 105411--105538 Score: 177
Period size: 66 Copynumber: 2.0 Consensus size: 65
105401 AAGTTTTTTG
* *
105411 GTTCTTTAATTGGGGGAGTTTC-TTTGGTTGGAAATGACTTTGAATGAGCAGGATTCCATTTTTG
1 GTTCTTTAATTGGAGGAGTTTCGTTT-ATTGGAAATGACTTTGAA-GAGCAGGATTCCATTTTTG
105475 TT
64 TT
* * * *
105477 GTTCTTTAATTGTAGGAGTTTCGTTTATTGGAAATGACTTTGAAGAGTAGGCTTCTATTTTT
1 GTTCTTTAATTGGAGGAGTTTCGTTTATTGGAAATGACTTTGAAGAGCAGGATTCCATTTTT
105539 TTGATGGTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
65 15 0.27
66 37 0.67
67 3 0.05
ACGTcount: A:0.21, C:0.09, G:0.25, T:0.45
Consensus pattern (65 bp):
GTTCTTTAATTGGAGGAGTTTCGTTTATTGGAAATGACTTTGAAGAGCAGGATTCCATTTTTGTT
Found at i:106090 original size:19 final size:20
Alignment explanation
Indices: 106066--106103 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
106056 GAGCTTGAAG
106066 TTTTCTGCTTCA-TCATTTT
1 TTTTCTGCTTCACTCATTTT
*
106085 TTTTCTGTTTCACTCATTT
1 TTTTCTGCTTCACTCATTT
106104 ATAAGCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.11, C:0.21, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTCTGCTTCACTCATTTT
Found at i:108076 original size:10 final size:10
Alignment explanation
Indices: 108061--108111 Score: 102
Period size: 10 Copynumber: 5.1 Consensus size: 10
108051 GGCACTTCTT
108061 GCTTTGCACA
1 GCTTTGCACA
108071 GCTTTGCACA
1 GCTTTGCACA
108081 GCTTTGCACA
1 GCTTTGCACA
108091 GCTTTGCACA
1 GCTTTGCACA
108101 GCTTTGCACA
1 GCTTTGCACA
108111 G
1 G
108112 ATACAATGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (10 bp):
GCTTTGCACA
Found at i:114843 original size:10 final size:9
Alignment explanation
Indices: 114827--114852 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
114817 AACTTAATAG
114827 TAAAAAAAA
1 TAAAAAAAA
114836 TAAAAAAAA
1 TAAAAAAAA
114845 TAAAAAAA
1 TAAAAAAA
114853 TAAGGTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:116601 original size:38 final size:38
Alignment explanation
Indices: 116559--116636 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
116549 TAAACAAACA
116559 AATTACAAACAAACTCACATTATGTGAGAGTTGAACCC
1 AATTACAAACAAACTCACATTATGTGAGAGTTGAACCC
*
116597 AATTACAAACAAACTCACATTCTGTGAGAGTTGAACCC
1 AATTACAAACAAACTCACATTATGTGAGAGTTGAACCC
116635 AA
1 AA
116637 GATCTCATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (38 bp):
AATTACAAACAAACTCACATTATGTGAGAGTTGAACCC
Found at i:120692 original size:2 final size:2
Alignment explanation
Indices: 120685--120713 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
120675 TAAACCCTCT
120685 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
120714 TTTCTTCTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:134003 original size:83 final size:79
Alignment explanation
Indices: 133861--134017 Score: 224
Period size: 83 Copynumber: 1.9 Consensus size: 79
133851 TTTTAAAAAA
* *
133861 TGAATAATCTGTTTTTGGTGTGGATTTGCTGTTGATGAGGTGCTAAACATGATAAATATTTGAAA
1 TGAATAATCTGTTTTTGGTGTGGATTTGCTATTAATGAGGTGCTAAACATGATAAATATTTGAAA
133926 ATGTGATAGAAAGT
66 ATGTGATAGAAAGT
* * * *
133940 TGAATAATCTGTTTTTGTTGTGTATTTGGGGCTAATTAATTAGGTGCTAAACATGATATATATTT
1 TGAATAATCTGTTTTTGGTGTGGATTT---GCT-ATTAATGAGGTGCTAAACATGATAAATATTT
134005 GAAAATGTGATAG
62 GAAAATGTGATAG
134018 GATTTGGAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
79 25 0.37
82 3 0.04
83 40 0.59
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (79 bp):
TGAATAATCTGTTTTTGGTGTGGATTTGCTATTAATGAGGTGCTAAACATGATAAATATTTGAAA
ATGTGATAGAAAGT
Found at i:147559 original size:15 final size:15
Alignment explanation
Indices: 147539--147570 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
147529 GCAAGTGAAA
147539 CTGACAGAGAAAAAG
1 CTGACAGAGAAAAAG
147554 CTGACAGAGAAAAAG
1 CTGACAGAGAAAAAG
147569 CT
1 CT
147571 ATCAATGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.25, T:0.09
Consensus pattern (15 bp):
CTGACAGAGAAAAAG
Found at i:149655 original size:40 final size:40
Alignment explanation
Indices: 149611--149693 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
149601 TTCAACTTAG
149611 TTTCAATTTGCTGACACTTTTTTCCATGAATGGAATGTAT
1 TTTCAATTTGCTGACACTTTTTTCCATGAATGGAATGTAT
149651 TTTCAATTTGCTGACACTTTTTTCCATGAATGGAATGTAT
1 TTTCAATTTGCTGACACTTTTTTCCATGAATGGAATGTAT
149691 TTT
1 TTT
149694 TCAGATATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (40 bp):
TTTCAATTTGCTGACACTTTTTTCCATGAATGGAATGTAT
Found at i:149967 original size:15 final size:15
Alignment explanation
Indices: 149947--149976 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
149937 GGTCTCGAGT
149947 TCGAATTAAATTATG
1 TCGAATTAAATTATG
149962 TCGAATTAAATTATG
1 TCGAATTAAATTATG
149977 GGATGGACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
TCGAATTAAATTATG
Found at i:150695 original size:3 final size:3
Alignment explanation
Indices: 150658--150682 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
150648 AAAAACAAAA
150658 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
150683 CTTACGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:166453 original size:3 final size:3
Alignment explanation
Indices: 166447--166484 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
166437 CTTGTTGTTG
*
166447 TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
166485 TTGAGAACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:185367 original size:20 final size:21
Alignment explanation
Indices: 185342--185381 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
185332 TCTTCCTTTC
185342 TTCTTTCTCTTCC-CTTTCTT
1 TTCTTTCTCTTCCGCTTTCTT
*
185362 TTCTTTCTTTTCCGCTTTCT
1 TTCTTTCTCTTCCGCTTTCT
185382 CTCTGATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.65
Consensus pattern (21 bp):
TTCTTTCTCTTCCGCTTTCTT
Found at i:186153 original size:90 final size:88
Alignment explanation
Indices: 186045--186218 Score: 269
Period size: 90 Copynumber: 2.0 Consensus size: 88
186035 AATTTTCTTG
*
186045 GTAAGCTTATAAAATTTTCATTAAACTTAAAAGCTTTTAAAATAGTTTTTTTTTAAATTTATTC-
1 GTAAGCTTATAAAATTTTCATTAAACTTAAAAGCTTTTAAAATAG--TTTTCTTAAATTTA-TCA
*
186109 AATTACCTCGTTTAAGATTTTTTTTT
63 AATCACCTCGTTTAAGATTTTTTTTT
* *
186135 GTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATCAAAT
1 GTAAGCTTATAAAATTTTCATTAAACTTAAAAGCTTTTAAAATAGTTTTCTTAAATTTATCAAAT
*
186200 CATCTCGTTTAAGATTTTT
66 CACCTCGTTTAAGATTTTT
186219 AGTGATATTA
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
87 2 0.03
88 33 0.42
90 43 0.55
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (88 bp):
GTAAGCTTATAAAATTTTCATTAAACTTAAAAGCTTTTAAAATAGTTTTCTTAAATTTATCAAAT
CACCTCGTTTAAGATTTTTTTTT
Found at i:186304 original size:20 final size:20
Alignment explanation
Indices: 186281--186319 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
186271 CCTTATAAGA
186281 TTTATAGTTAA-CTTATGAAT
1 TTTATAG-TAACCTTATGAAT
186301 TTTATAGTAACCTTATGAA
1 TTTATAGTAACCTTATGAA
186320 GTATTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTATAGTAACCTTATGAAT
Found at i:187830 original size:19 final size:19
Alignment explanation
Indices: 187819--187855 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
187809 AATTTTTAAG
187819 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
187838 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
187856 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:188610 original size:39 final size:39
Alignment explanation
Indices: 188567--188674 Score: 96
Period size: 40 Copynumber: 2.7 Consensus size: 39
188557 TTTTGCTAAC
188567 ATAATTACTAATTGATTGATTTATTTATGGCAAAATTAA
1 ATAATTACTAATTGATTGATTTATTTATGGCAAAATTAA
** * *
188606 ATAATTA-TGAATCAATT-A-TAACTTTGATTGGCAAAGTTAA
1 ATAATTACT-AATTGATTGATTTA-TTT-A-TGGCAAAATTAA
* *
188646 CTAATGACTAACTTGATTGATTTATTTAT
1 ATAATTACTAA-TTGATTGATTTATTTAT
188675 TTAGCATGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
37 2 0.04
38 5 0.10
39 14 0.27
40 19 0.37
41 6 0.12
42 4 0.08
43 2 0.04
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (39 bp):
ATAATTACTAATTGATTGATTTATTTATGGCAAAATTAA
Found at i:188986 original size:164 final size:165
Alignment explanation
Indices: 188752--189214 Score: 750
Period size: 164 Copynumber: 2.8 Consensus size: 165
188742 TGATTGATTT
* * * *
188752 ATTTATGGTAAAATTAAATAATCATCAATCAGTTATAACTTTGATTGGCAAAGTTAACTAATGAC
1 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGGCAAAATTAACTAACGAC
* * * *
188817 TAACTTGATTCATTTGTCTATTTAGCATGTTCAATAATTAATTTTTTTGGTAACATAATCACTAA
66 TAACTTGATTCATTTATTTATTTAGCATGTTCAATAATTTATTTTTTTGGTAACATAATTACTAA
188882 TTGATTTATTTATTTATGGTAA-TTTTTGGTAGCG
131 TTGATTTATTTATTTATGGTAATTTTTTGGTAGCG
* **
188916 ATTTATGGTAAAATTAAATAATTATCAATCAATTAAAACTTTGATTCACAAAATTAACTAACGAC
1 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGGCAAAATTAACTAACGAC
*
188981 TAACTTGGATTCATTTATTTATTTACCATGTTCAATAATTTA-TTTTTTGGTAACATAATTACTA
66 TAACTT-GATTCATTTATTTATTTAGCATGTTCAATAATTTATTTTTTTGGTAACATAATTACTA
189045 ATTGATTTATTTATTTATGGTAATTTTTTGGTAGCG
130 ATTGATTTATTTATTTATGGTAATTTTTTGGTAGCG
* *
189081 ATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACAAC
1 ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGGCAAAATTAACTAACGAC
*
189146 TAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTATTTTTTTGCTAACATAATTACT
66 TAACTTGATTCATTTATTTATTTAGCATGTTCAAT-AA-TTTATTTTTTTGGTAACATAATTACT
189211 AATT
129 AATT
189215 AATTCGTTTA
Statistics
Matches: 275, Mismatches: 19, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
164 136 0.49
165 111 0.40
166 4 0.01
167 24 0.09
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.44
Consensus pattern (165 bp):
ATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGGCAAAATTAACTAACGAC
TAACTTGATTCATTTATTTATTTAGCATGTTCAATAATTTATTTTTTTGGTAACATAATTACTAA
TTGATTTATTTATTTATGGTAATTTTTTGGTAGCG
Found at i:189521 original size:142 final size:142
Alignment explanation
Indices: 189246--189606 Score: 494
Period size: 142 Copynumber: 2.6 Consensus size: 142
189236 ATTATAGGAG
* * * * * *
189246 TAACTTTTATTGGCAAAGTTGACTT-AGGACTAACTTGGTTCATTTGTTTATTTAGCATGTTGAA
1 TAACTTTGATTGGCAAAGTT-AATTAAGGACTAATTTGATTCATTTATTTATTTAGCATGTTCAA
* * ** *
189310 TCAGTTTA--TTTTTGCTAACATAATTACTAATTGATACATTTATTTATGGAAAAATTTAATAAT
65 TCAATTTATTTTTTTGCTAACATAATTACTAATTGATACATTTATTTATAGAAAAATCAAATAAC
* *
189373 CATCAATTAGTTA
130 CATCAATCAATTA
* * *
189386 TAACTTTGATTGGCAAAGTTAATTAACGACTAATTTGATTTATTTATTTATTTAGTATGTTCAAT
1 TAACTTTGATTGGCAAAGTTAATTAAGGACTAATTTGATTCATTTATTTATTTAGCATGTTCAAT
* * * *
189451 CAATTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATCACC
66 CAATTTATTTTTTTGCTAACATAATTACTAATTGATACATTTATTTATAGAAAAATCAAATAACC
189516 ATCAATCAATTA
131 ATCAATCAATTA
* *
189528 TAACTTTGATTGACAAAGTTGATTAAGGACTAATTTGATTCATTTATTTATTTAGCATGTTCAAT
1 TAACTTTGATTGGCAAAGTTAATTAAGGACTAATTTGATTCATTTATTTATTTAGCATGTTCAAT
189593 CAATTTATTTTTTT
66 CAATTTATTTTTTT
189607 AGTGGTTAAA
Statistics
Matches: 193, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
139 3 0.02
140 58 0.30
142 132 0.68
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (142 bp):
TAACTTTGATTGGCAAAGTTAATTAAGGACTAATTTGATTCATTTATTTATTTAGCATGTTCAAT
CAATTTATTTTTTTGCTAACATAATTACTAATTGATACATTTATTTATAGAAAAATCAAATAACC
ATCAATCAATTA
Found at i:189709 original size:172 final size:172
Alignment explanation
Indices: 189448--189778 Score: 497
Period size: 172 Copynumber: 1.9 Consensus size: 172
189438 TAGTATGTTC
* *
189448 AATCAATTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATC
1 AATCAAGTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATA
* * * *
189513 ACCATCAATCAATTATAACTTTGATTGACAAAGTTGATTAAGGAC-TAATTTGATTCATTTATTT
66 ACCATCAATCAATTATAACTTTGATTGACAAAGTTAACTAA-CACTTAACTTGATTCATTTATTT
189577 ATTTAGCATGTTCAATCAATTTATTTTTTTAGTGGTTAAAAAA
130 ATTTAGCATGTTCAATCAATTTATTTTTTTAGTGGTTAAAAAA
* *
189620 AATCAAGTTATTTTTTTGAC-AACATAATTACTAATTGATT-TATTTATTTATGGCAAAATTAAA
1 AATCAAGTTATTTTTTTG-CTAACATAATTACTAATTGATTCT-TTTATTTATAGCAAAATCAAA
* * * *
189683 TAATCATCCATCAATTATAACTTTGATTGGCAAAGTTAACTCACACTTAACTTGATTCATTTATT
64 TAACCATCAATCAATTATAACTTTGATTGACAAAGTTAACTAACACTTAACTTGATTCATTTATT
*
189748 TATTTTGCATGTTCAATCAATTTATTTTTTT
129 TATTTAGCATGTTCAATCAATTTATTTTTTT
189779 CAACATAATT
Statistics
Matches: 143, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
171 3 0.02
172 139 0.97
173 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (172 bp):
AATCAAGTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATA
ACCATCAATCAATTATAACTTTGATTGACAAAGTTAACTAACACTTAACTTGATTCATTTATTTA
TTTAGCATGTTCAATCAATTTATTTTTTTAGTGGTTAAAAAA
Done.