Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000967.1 Hibiscus syriacus cultivar Beakdansim tig00001929_pilon, 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: 63506
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1835 original size:4 final size:4
Alignment explanation
Indices: 1826--1857 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1816 CATCCTCAAC
1826 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1858 CCATTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:8354 original size:262 final size:262
Alignment explanation
Indices: 7879--8447 Score: 769
Period size: 262 Copynumber: 2.2 Consensus size: 262
7869 AAAAAACAAG
* **
7879 AAAAGTAATTTTCAATTTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAA
1 AAAAGCAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAA
*
7944 GCAGTTTCAAACGTTTCTTACCCTGTAGACTATTTCCAAAATTGGTAAGTCCTTCGGGCAATCAA
66 GCAGTTTCAAACGTTTCTTACCCAGTAGACTATTTCCAAAATTGGTAAGTCCTTCGGGCAATCAA
* * ** *
8009 TAAGTCTTTCGCATATGATGATTAAATCCTTTAGGTCATCAGTCTGTCTTTCGAACAAGACGATG
131 TAAGTCTTTCGCACATGATGATTAAATCCTTGAGGTCATCAGTCAATCTTTCGAACAAGACGATA
* * * ** *
8074 AGTCCTTTGGGCCATCTATAAGACCTTTGGGCAAGATGTTTTCATAT-GATGTTTGTAA-AAAAT
196 AGTCATTCGAGCCATCTATAAGACCTTCAGGCAAGATGTTTTCATATAG-TATTTGTAAGAAAAT
8137 GAT
260 GAT
*
8140 AAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTTCAGAAAATGAAATTTTTGAAAAGTAAGAA
1 AAAAGCAATTTTCAAAGTTTCTCATTTAAT-ATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAA
* *
8205 AGC-GATTTCCAAA-GTTTCTTACCCAGTAGACTATTTCCAAAATTGGTAAGTCCTTTGGGCCAT
65 AGCAG-TTT-CAAACGTTTCTTACCCAGTAGACTATTTCCAAAATTGGTAAGTCCTTCGGGCAAT
* * *
8268 CAGTAAGTCTTTCG-AGCATGATGATTAAATCCTTGGGGTCATCTGTCAATCTTTC-AAGCAAGA
128 CAATAAGTCTTTCGCA-CATGATGATTAAATCCTTGAGGTCATCAGTCAATCTTTCGAA-CAAGA
* * **
8331 GGATAAGTCATTCGAGTCATCTATAAGACCTTCAGGCTTGATGTTTTCATATAGTATTTGTAAGA
191 CGATAAGTCATTCGAGCCATCTATAAGACCTTCAGGCAAGATGTTTTCATATAGTATTTGTAAGA
*
8396 GAATGAT
256 AAATGAT
* *
8403 AAAA-CGATTTTCAAAGTTTCTCATTTAAAATTTTCA-AAAAT-AAAT
1 AAAAGCAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAAT
8448 AAAAAATGAT
Statistics
Matches: 272, Mismatches: 29, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
259 4 0.01
260 5 0.02
261 37 0.14
262 210 0.77
263 16 0.06
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (262 bp):
AAAAGCAATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAA
GCAGTTTCAAACGTTTCTTACCCAGTAGACTATTTCCAAAATTGGTAAGTCCTTCGGGCAATCAA
TAAGTCTTTCGCACATGATGATTAAATCCTTGAGGTCATCAGTCAATCTTTCGAACAAGACGATA
AGTCATTCGAGCCATCTATAAGACCTTCAGGCAAGATGTTTTCATATAGTATTTGTAAGAAAATG
AT
Found at i:8512 original size:25 final size:25
Alignment explanation
Indices: 8468--8532 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
8458 TAAAAGGGGG
*
8468 GAGAAAAATGAAAAATGAAAAAATTA
1 GAGAAAAA-CAAAAATGAAAAAATTA
8494 GAGAAGAAA-AAAAATGAAAAAATTA
1 GAGAA-AAACAAAAATGAAAAAATTA
8519 GAGAAAAACAAAAA
1 GAGAAAAACAAAAA
8533 GATAGAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
24 3 0.08
25 26 0.70
26 5 0.14
27 3 0.08
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (25 bp):
GAGAAAAACAAAAATGAAAAAATTA
Found at i:10664 original size:8 final size:8
Alignment explanation
Indices: 10651--10713 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
10641 ATATGTATAC
10651 ATATTTTT
1 ATATTTTT
**
10659 ATATTTAC
1 ATATTTTT
10667 ATATTTTT
1 ATATTTTT
10675 ATATTTTT
1 ATATTTTT
10683 AT-TTTCTT
1 ATATTT-TT
10691 -TACTTTATT
1 ATA-TTT-TT
10700 AT-TTTTT
1 ATATTTTT
10707 AT-TTTTT
1 ATATTTTT
10714 TCTTAATCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
7 13 0.28
8 27 0.59
9 5 0.11
10 1 0.02
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (8 bp):
ATATTTTT
Found at i:10669 original size:16 final size:16
Alignment explanation
Indices: 10648--10680 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10638 CTTATATGTA
10648 TACATATTTTTATATT
1 TACATATTTTTATATT
10664 TACATATTTTTATATT
1 TACATATTTTTATATT
10680 T
1 T
10681 TTATTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TACATATTTTTATATT
Found at i:13453 original size:95 final size:95
Alignment explanation
Indices: 13277--13477 Score: 262
Period size: 95 Copynumber: 2.1 Consensus size: 95
13267 CCAAAATTAT
* * * *
13277 ATTATATACATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACACCCTGACTTTA
1 ATTATA-ATATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGCTTAAACACCCTGAATTTA
* * *
13342 TGGATAAGATTTAGCTAGCCTGATAAAGATG
65 TGCATAAGATTCAGCTAGCCTAATAAAGATG
* **
13373 ATTTTAATATACAATAAAGCTTGAAG-TATCCCTCTAAAGCAATTGCTTAAATGTCCC-GAATTT
1 ATTATAATATACAATAAAGCTTG-AGTTATCCCTCTAAAGCAATTGCTTAAA-CACCCTGAATTT
*
13436 ATGCATAAGATTCAGCTAGCCTAATAAAGGTG
64 ATGCATAAGATTCAGCTAGCCTAATAAAGATG
13468 ATTATAATAT
1 ATTATAATAT
13478 TGAGTTGTCT
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
95 81 0.89
96 10 0.11
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTATCCCTCTAAAGCAATTGCTTAAACACCCTGAATTTAT
GCATAAGATTCAGCTAGCCTAATAAAGATG
Found at i:14433 original size:84 final size:84
Alignment explanation
Indices: 14291--15394 Score: 1267
Period size: 84 Copynumber: 13.1 Consensus size: 84
14281 CAAGCACCTT
* * * * *
14291 CAACAAAAGTCCTTCAAGTTCGATTACACTCAGCTCAAAGGCACAACA-TTGACTGCATAGCTTA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTG-CAGCATAGCTCA
*
14355 AGGCCAGAAGGGCTATCTGC
65 AGGCAAGAAGGGCTATCTGC
* *
14375 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAAGAACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
14440 GGCAATAAGGGCTATATGC
66 GGCAAGAAGGGCTATCTGC
* * * * * * * *
14459 CAATAAAAGACCTTCTAGTTTGATTACACTTAGCTCAAATGCACATAATTTGTAGCATAACTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * **
14524 GGCAAAAAGGGTTATCTTT
66 GGCAAGAAGGGCTATCTGC
* * ** *
14543 CAGCAAAATA-CTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTTGCATAGCTAAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
** *
14607 GGTGAGAAGGGTTATCTGC
66 GGCAAGAAGGGCTATCTGC
* * * *
14626 CAACAAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATAATTTGCAGCATAACTAAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
14691 GGTAAGAAGGGCTATCTGC
66 GGCAAGAAGGGCTATCTGC
* * ** * *
14710 CAACAAAAGACCTTCGAGTTCAATTACACTCAGCTCAAGGGCATGTCAAATTTGCAGCATAACTT
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTC
** *
14775 AATTCGAGAAGGGCTATCTGC
64 AAGGCAAGAAGGGCTATCTGC
* * * *
14796 CAGCAAAATACCTTCGATTTCGATTACACTCAGCTCAAAGGCACATCATTTGGAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
14861 GGCAAAAAGGGGCTATCTGC
66 GGCAAGAA-GGGCTATCTGC
* * *
14881 CAACAGAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * *
14946 GGAAATAAGGGCTATCTAC
66 GGCAAGAAGGGCTATCTGC
* * * * * *
14965 CAACAGAAGACTTTCGAGTTTGATTACACTCAACTCAAAGGCACATCATTTACAGTATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * *
15030 GGCAAAAAGGGTTATCTAC
66 GGCAAGAAGGGCTATCTGC
* ** * * *
15049 CAATAAAAGATTTTCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCCGTATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
15114 GGCAAGAAGGGCTATCTGC
66 GGCAAGAAGGGCTATCTGC
* * * * *
15133 TATCAGAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATTATTTTCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
15198 GGCAAGAAGGGTTATCTTC
66 GGCAAGAAGGGCTATCTGC
* * * * * * *
15217 TAATAAAAGACCTTCGTGTTCGATTAGACTCAGATCAAAGGCACATTATTTGCAGCATAACTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
15282 GGTAAGAAGGGTTATCTGC
66 GGCAAGAAGGGCTATCTGC
* * ** * *
15301 CAACAAAAGACCTTCGAGTTCAATTACACTCAGCTCAAGGGCATGTCAAATTTGCAACATAGCTT
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAGCTC
** ** *
15366 AATTCAAGAAAAGCTATCTGT
64 AAGGCAAGAAGGGCTATCTGC
15387 CAACAAAA
1 CAACAAAA
15395 ATTTTTGAGT
Statistics
Matches: 871, Mismatches: 142, Indels: 12
0.85 0.14 0.01
Matches are distributed among these distances:
83 68 0.08
84 618 0.71
85 78 0.09
86 107 0.12
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (84 bp):
CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
GGCAAGAAGGGCTATCTGC
Found at i:17265 original size:12 final size:13
Alignment explanation
Indices: 17248--17276 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
17238 AAATCGAGTT
17248 TTTTAATTT-TAA
1 TTTTAATTTCTAA
17260 TTTTAATTTCTAA
1 TTTTAATTTCTAA
17273 TTTT
1 TTTT
17277 CGTAAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAATTTCTAA
Found at i:19125 original size:36 final size:33
Alignment explanation
Indices: 19072--19139 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 33
19062 TTTAAAATAT
*
19072 TTTAGTCCTAATTTAGATTACTTTATATTTTAGA
1 TTTAGTCCTAATTTAGATTACTTT-TAATTTAGA
*
19106 TTTAGTCCTTAAATTTAGATTTCTTTTAATTTAG
1 TTTAGTCC-T-AATTTAGATTACTTTTAATTTAG
19140 TCCATAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 8 0.27
35 8 0.27
36 14 0.47
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (33 bp):
TTTAGTCCTAATTTAGATTACTTTTAATTTAGA
Found at i:19301 original size:2 final size:2
Alignment explanation
Indices: 19294--19330 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19284 AACACTTTGA
19294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19331 GTTTTTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19335 original size:56 final size:54
Alignment explanation
Indices: 19253--19366 Score: 176
Period size: 56 Copynumber: 2.1 Consensus size: 54
19243 GCCACTTTGA
*
19253 ATATATATATATCTAATATATAGTTTTTGAAAACACTTT-GAATATATATATATAT
1 ATATATATATATATAATATATAGTTTTTGAAAACACTTTCGAA-ATATATATA-AT
*
19308 ATATATATATATATATATATATAGTTTTTGAAAACATTTTCGAAATATATATAAT
1 ATATATATATATATA-ATATATAGTTTTTGAAAACACTTTCGAAATATATATAAT
19363 ATAT
1 ATAT
19367 GGTTTTTGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
55 20 0.36
56 32 0.58
57 3 0.05
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (54 bp):
ATATATATATATATAATATATAGTTTTTGAAAACACTTTCGAAATATATATAAT
Found at i:19421 original size:28 final size:29
Alignment explanation
Indices: 19392--19449 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
19382 TTTAAAATAT
19392 ATATAAAT--TATATAG-TTTTTGAAAAC
1 ATATAAATAATATATAGTTTTTTGAAAAC
19418 ATATAAATAATATATAGTTTTTTTGAAAAC
1 ATATAAATAATATATAG-TTTTTTGAAAAC
19448 AT
1 AT
19450 TTTGGAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 8 0.29
28 7 0.25
30 13 0.46
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (29 bp):
ATATAAATAATATATAGTTTTTTGAAAAC
Found at i:19445 original size:68 final size:67
Alignment explanation
Indices: 19352--19541 Score: 260
Period size: 69 Copynumber: 2.8 Consensus size: 67
19342 CATTTTCGAA
* *
19352 ATATATATAATATATGGTTTTTGAAAATATTTT-AAAATATATATAAATTATATAGTTT-TTGAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAAA-TATATAGTTTGTTGAA
19415 AAC
65 AAC
* * *
19418 ATATAAATAATATATAGTTTTTTTGAAAACATTTTGGAAATATATATATAATATATGGTTTGTTG
1 ATATATATAATATATAG--TTTTTGAAAACATTTTGAAAATATATATA-AATATATAGTTTGTTG
19483 AAAAC
63 AAAAC
*
19488 ATATATATAATATATAGTTTTTGAAAAACATTTTGAAAGTATATAT-AATATATA
1 ATATATATAATATATAGTTTTTG-AAAACATTTTGAAAATATATATAAATATATA
19542 ATTTTAAAAT
Statistics
Matches: 109, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
66 15 0.14
67 7 0.06
68 21 0.19
69 40 0.37
70 26 0.24
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (67 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAAATATATAGTTTGTTGAAA
AC
Found at i:19453 original size:41 final size:40
Alignment explanation
Indices: 19408--19489 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
19398 ATTATATAGT
* *
19408 TTTTGAAAACATATAAATAATATATAGTTTTTTTGAAAACA
1 TTTTGAAAACATATAAATAATATAT-GGTTTGTTGAAAACA
* * *
19449 TTTTGGAAATATATATATAATATATGGTTTGTTGAAAACA
1 TTTTGAAAACATATAAATAATATATGGTTTGTTGAAAACA
19489 T
1 T
19490 ATATATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 14 0.39
41 22 0.61
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (40 bp):
TTTTGAAAACATATAAATAATATATGGTTTGTTGAAAACA
Found at i:19493 original size:31 final size:28
Alignment explanation
Indices: 19449--19514 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
19439 TTTGAAAACA
* * *
19449 TTTTGGAAATATATATATAATATATGGT
1 TTTTGAAAACATATATATAATATATAGT
19477 TTGTTGAAAACATATATATAATATATAGT
1 TT-TTGAAAACATATATATAATATATAGT
19506 TTTTGAAAA
1 TTTTGAAAA
19515 ACATTTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 9 0.26
29 25 0.74
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (28 bp):
TTTTGAAAACATATATATAATATATAGT
Found at i:19661 original size:16 final size:16
Alignment explanation
Indices: 19618--19685 Score: 63
Period size: 16 Copynumber: 4.2 Consensus size: 16
19608 TATAATATAG
19618 TTTTTTTA-TTATTTAT
1 TTTTTTTATTTA-TTAT
19634 TTATTTACTTATTTATTAT
1 TT-TTT--TTATTTATTAT
*
19653 TTTTTTTATTTACTA-
1 TTTTTTTATTTATTAT
19668 -TTTTTTATTT-TTAT
1 TTTTTTTATTTATTAT
19682 TTTT
1 TTTT
19686 AGGTCCAAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
13 2 0.05
14 10 0.23
15 3 0.07
16 11 0.25
17 3 0.07
18 3 0.07
19 9 0.20
20 3 0.07
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTATTTATTAT
Found at i:19678 original size:23 final size:25
Alignment explanation
Indices: 19619--19683 Score: 98
Period size: 23 Copynumber: 2.6 Consensus size: 25
19609 ATAATATAGT
19619 TTTTTTATTATTTATTTATTTACTTA
1 TTTTTTATT-TTTATTTATTTACTTA
*
19645 TTTATTATTTTT-TTTATTTAC-TA
1 TTTTTTATTTTTATTTATTTACTTA
19668 TTTTTTATTTTTATTT
1 TTTTTTATTTTTATTT
19684 TTAGGTCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 13 0.36
24 12 0.33
25 3 0.08
26 8 0.22
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTTATTTTTATTTATTTACTTA
Found at i:19685 original size:7 final size:7
Alignment explanation
Indices: 19619--19685 Score: 50
Period size: 7 Copynumber: 9.7 Consensus size: 7
19609 ATAATATAGT
19619 TTTTTTA
1 TTTTTTA
*
19626 TTATTTA
1 TTTTTTA
19633 TTTATTTA
1 TTT-TTTA
*
19641 CTTATTTA
1 -TTTTTTA
*
19649 -TTATT-
1 TTTTTTA
19654 TTTTTTA
1 TTTTTTA
**
19661 TTTACTA
1 TTTTTTA
19668 TTTTTTA
1 TTTTTTA
19675 -TTTTTA
1 TTTTTTA
19681 TTTTT
1 TTTTT
19686 AGGTCCAAGT
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
6 13 0.29
7 22 0.49
8 8 0.18
9 2 0.04
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:31325 original size:23 final size:23
Alignment explanation
Indices: 31294--31401 Score: 123
Period size: 23 Copynumber: 4.8 Consensus size: 23
31284 CTATGCGCTA
* *
31294 GGTATCGATACCCCCTTTGAATG
1 GGTACCGATACCCTCTTTGAATG
* *
31317 GGTACCGATACCCCCTTTAAATG
1 GGTACCGATACCCTCTTTGAATG
* *
31340 GGTACCGATA-CCTATTTGAATT
1 GGTACCGATACCCTCTTTGAATG
* *
31362 GGTATCGATACCCTCTATG-A-G
1 GGTACCGATACCCTCTTTGAATG
31383 GGTACCGATACCCTCTTTG
1 GGTACCGATACCCTCTTTG
31402 GGTTCTGGTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
21 17 0.24
22 18 0.25
23 37 0.51
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (23 bp):
GGTACCGATACCCTCTTTGAATG
Found at i:32462 original size:15 final size:15
Alignment explanation
Indices: 32442--32471 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
32432 CTAATGCATT
32442 TGGATTAGATAATGA
1 TGGATTAGATAATGA
32457 TGGATTAGATAATGA
1 TGGATTAGATAATGA
32472 AAATGAAATA
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:0.00, G:0.27, T:0.33
Consensus pattern (15 bp):
TGGATTAGATAATGA
Found at i:33628 original size:33 final size:33
Alignment explanation
Indices: 33586--33653 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
33576 AAAGTGGGAG
* * *
33586 AAGTTGTTATAGTAAGGGGGAGTAATTTTTTAA
1 AAGTTGTTATAGTAAAGGCGAGTAATTTTTCAA
33619 AAGTTGTTATAGTAAAGGCGAGTAATTTTTCAA
1 AAGTTGTTATAGTAAAGGCGAGTAATTTTTCAA
33652 AA
1 AA
33654 TTACTTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (33 bp):
AAGTTGTTATAGTAAAGGCGAGTAATTTTTCAA
Found at i:40418 original size:20 final size:20
Alignment explanation
Indices: 40394--40509 Score: 160
Period size: 20 Copynumber: 5.8 Consensus size: 20
40384 TTTCCCACAC
* * *
40394 ATTTGTAAAGCCTACGGGTC
1 ATTTGTAAAACCTTCGGGTA
* * * *
40414 ATTTGTAAAGCCTCCAGGTC
1 ATTTGTAAAACCTTCGGGTA
40434 ATTTGTAAAACCTTCGGGTA
1 ATTTGTAAAACCTTCGGGTA
40454 ATTTGTAAAACCTTCGGGTA
1 ATTTGTAAAACCTTCGGGTA
40474 ATTTGTAAAACCTTCGGGTA
1 ATTTGTAAAACCTTCGGGTA
*
40494 ATTTGTAAATCCTTCG
1 ATTTGTAAAACCTTCG
40510 AGTCATCTGT
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 89 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (20 bp):
ATTTGTAAAACCTTCGGGTA
Found at i:40783 original size:36 final size:36
Alignment explanation
Indices: 40738--40956 Score: 280
Period size: 36 Copynumber: 6.1 Consensus size: 36
40728 TTCTCAAGTT
* * *
40738 AAGTCATTCAAATTCAACATTCACGGAAGAGTAGTG
1 AAGTTATTCAAATTCAACCTTCACGAAAGAGTAGTG
*
40774 AAGTTATTCAAATTCAACCTTCACGGAAGAGTAGTG
1 AAGTTATTCAAATTCAACCTTCACGAAAGAGTAGTG
*
40810 AAGTCATTCAAATTCAACCTTCACGAAAGAGTAGTG
1 AAGTTATTCAAATTCAACCTTCACGAAAGAGTAGTG
*
40846 AA-TTCATCCAAATTCAACCTTCACGAAAGAGTAGTG
1 AAGTT-ATTCAAATTCAACCTTCACGAAAGAGTAGTG
* * *
40882 AAGTAATTCAAATTCAACCTTAACGAAAGAGTTGTG
1 AAGTTATTCAAATTCAACCTTCACGAAAGAGTAGTG
* * * * *
40918 AAGTTGA-TCAAATTTAGCTTTCACAAAAGAATAGTG
1 AAGTT-ATTCAAATTCAACCTTCACGAAAGAGTAGTG
40954 AAG
1 AAG
40957 CCAATCATTT
Statistics
Matches: 162, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
35 1 0.01
36 159 0.98
37 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (36 bp):
AAGTTATTCAAATTCAACCTTCACGAAAGAGTAGTG
Found at i:41216 original size:3 final size:3
Alignment explanation
Indices: 41210--41239 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41200 ATTATATTAT
41210 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41240 TTATTCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41352 original size:18 final size:19
Alignment explanation
Indices: 41329--41367 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
41319 GACTCAATTT
41329 ATAACCC-GTTCAGACCCA
1 ATAACCCAGTTCAGACCCA
*
41347 ATAACCCAGTTCAGGCCCA
1 ATAACCCAGTTCAGACCCA
41366 AT
1 AT
41368 CCCAGCAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.33, C:0.36, G:0.13, T:0.18
Consensus pattern (19 bp):
ATAACCCAGTTCAGACCCA
Found at i:44391 original size:149 final size:148
Alignment explanation
Indices: 43959--44411 Score: 498
Period size: 149 Copynumber: 3.0 Consensus size: 148
43949 TGCTCTACGT
* * * * * *
43959 AGATTAAGTAGCGTCAAGAAGGAGTCTACCTACCAAGGAGACGAGCCAGATATATGCATGTTGAG
1 AGATGAAGTAGAGTCAAGAGGGAGTCTACCTACCAAGGAGACGATCCAGACATTTGCATGTTGAG
* * * *
44024 GTAACAAGTTGGAATCGAGATGATTTGATGTCGAAGCCAACAATTGAAGATCACAAGCTAGCTCG
66 GTAACAAGTTGGAATCGAGACGATTTGATGTCGAAGCCAATAATTGAAGATCA-AAACCAGCTCG
* *
44089 AAATATTTCTGGAAATAAG
130 AAAGATTTCTGGAAATAGG
* * *
44108 AGATGAAGTAGAGTCAAGAGGGAGTCTAGCTACCAAGGAGACGATCCAGACATTTACCTGTTGAG
1 AGATGAAGTAGAGTCAAGAGGGAGTCTACCTACCAAGGAGACGATCCAGACATTTGCATGTTGAG
* * * * *
44173 CTAACAAGTTGGAATCGAGACGATTTGATG-CTGAAGCCAATAGTTAAAGATGAAAAACCAGTTC
66 GTAACAAGTTGGAATCGAGACGATTTGATGTC-GAAGCCAATAATTGAAGAT-CAAAACCAGCTC
* *
44237 AAAAGATTTATGGAAATAGG
129 GAAAGATTTCTGGAAATAGG
* * * *
44257 AGATGAAGTAGGAG-CTAGAGGGAGTCTATCTACCAAGGAGACGATCCGGACATTTGCATGCTGA
1 AGATGAAGTA-GAGTCAAGAGGGAGTCTACCTACCAAGGAGACGATCCAGACATTTGCATGTTGA
* * * * ** * * * *
44321 GGTAACAAGTTAGACTTGATACGATTCAATGTCGAAACCAATAATTGAATATCATGAACCAACTC
65 GGTAACAAGTTGGAATCGAGACGATTTGATGTCGAAGCCAATAATTGAAGATCA-AAACCAGCTC
*
44386 GAAAGACTTCT-GAAAGTAGG
129 GAAAGATTTCTGGAAA-TAGG
44406 AGATGA
1 AGATGA
44412 GGTAAAAGCT
Statistics
Matches: 252, Mismatches: 46, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
148 6 0.02
149 241 0.96
150 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (148 bp):
AGATGAAGTAGAGTCAAGAGGGAGTCTACCTACCAAGGAGACGATCCAGACATTTGCATGTTGAG
GTAACAAGTTGGAATCGAGACGATTTGATGTCGAAGCCAATAATTGAAGATCAAAACCAGCTCGA
AAGATTTCTGGAAATAGG
Found at i:45907 original size:29 final size:29
Alignment explanation
Indices: 45870--45925 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
45860 AAGATATAGC
45870 AAAAAGAAAAAGGAGAAAAAAT-GAAAATG
1 AAAAAGAAAAAGGA-AAAAAATAGAAAATG
* *
45899 AAAATGAAAAATGAAAAAAATAGAAAA
1 AAAAAGAAAAAGGAAAAAAATAGAAAA
45926 AAAACAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (29 bp):
AAAAAGAAAAAGGAAAAAAATAGAAAATG
Found at i:46961 original size:32 final size:32
Alignment explanation
Indices: 46915--46978 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
46905 AAGAAACGAT
46915 GAATGATGGGGCATCTTTGGAGATTCAACATC
1 GAATGATGGGGCATCTTTGGAGATTCAACATC
* * *
46947 GAATGTTGGTGCATCTTTGGGGATTCAACATC
1 GAATGATGGGGCATCTTTGGAGATTCAACATC
46979 CAAAGATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (32 bp):
GAATGATGGGGCATCTTTGGAGATTCAACATC
Found at i:47410 original size:36 final size:36
Alignment explanation
Indices: 47305--47492 Score: 171
Period size: 36 Copynumber: 5.1 Consensus size: 36
47295 CACATATGAT
* * *
47305 AGTTTTCTTAAAGAACAATTTTTGTCTCATTTGAGAC
1 AGTTTTCTTTAA-AACAAATTTTGTCTCACTTGAGAC
* * * ** *
47342 AATTTTCCTTAAAACAAAATTAATCTCACTTGAGAT
1 AGTTTTCTTTAAAACAAATTTTGTCTCACTTGAGAC
* * *
47378 TGTTTTCTTTAAAACAAATTTTGTCTCCCTTGAGAT
1 AGTTTTCTTTAAAACAAATTTTGTCTCACTTGAGAC
* * * *
47414 AGTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGAC
1 AGTTTTCTTTAAAACAAA-TTTTGTCTCACTTGAGAC
* *
47451 AG-TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGAC
1 AGTTTTCT-TTAAAACAAA-TTTTGTCTCACTTGAGAC
47488 AGTTT
1 AGTTT
47493 CCCTTGAAAC
Statistics
Matches: 124, Mismatches: 24, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
36 64 0.52
37 58 0.47
38 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.41
Consensus pattern (36 bp):
AGTTTTCTTTAAAACAAATTTTGTCTCACTTGAGAC
Found at i:47446 original size:22 final size:22
Alignment explanation
Indices: 47418--47484 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 22
47408 TGAGATAGTT
47418 TCCCTTGAAACAAAGTTTTGTC
1 TCCCTTGAAACAAAGTTTTGTC
*
47440 TCCCTTGAGAC--AG--TT-TC
1 TCCCTTGAAACAAAGTTTTGTC
47457 T--CTTGAAACAAAGTTTTGTC
1 TCCCTTGAAACAAAGTTTTGTC
*
47477 TCTCTTGA
1 TCCCTTGA
47485 GACAGTTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
15 7 0.19
17 5 0.14
18 2 0.06
19 2 0.06
20 5 0.14
22 15 0.42
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (22 bp):
TCCCTTGAAACAAAGTTTTGTC
Found at i:47446 original size:37 final size:37
Alignment explanation
Indices: 47389--47503 Score: 196
Period size: 37 Copynumber: 3.1 Consensus size: 37
47379 GTTTTCTTTA
*
47389 AAACAAA-TTTTGTCTCCCTTGAGATAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTTG
*
47425 AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTTG
*
47462 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTTG
47499 AAACA
1 AAACA
47504 CCAATCTTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 7 0.09
37 67 0.91
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (37 bp):
AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTTG
Found at i:47491 original size:20 final size:20
Alignment explanation
Indices: 47431--47492 Score: 53
Period size: 22 Copynumber: 3.2 Consensus size: 20
47421 CTTGAAACAA
*
47431 AGTTTTGTCTCCCTTGAGAC
1 AGTTTTGTCTCTCTTGAGAC
*
47451 AG---T-T-TCTCTTGAAAC
1 AGTTTTGTCTCTCTTGAGAC
47466 AAAGTTTTGTCTCTCTTGAGAC
1 --AGTTTTGTCTCTCTTGAGAC
47488 AGTTT
1 AGTTT
47493 CCCTTGAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 14
0.65 0.06 0.29
Matches are distributed among these distances:
15 9 0.28
16 1 0.03
17 3 0.09
20 8 0.25
21 1 0.03
22 10 0.31
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (20 bp):
AGTTTTGTCTCTCTTGAGAC
Found at i:47523 original size:30 final size:30
Alignment explanation
Indices: 47489--47631 Score: 171
Period size: 30 Copynumber: 4.6 Consensus size: 30
47479 TCTTGAGACA
**
47489 GTTTCCCTTGAAACACCAATCTTTGAATCT
1 GTTTCCCTTGAAACAAAAATCTTTGAATCT
* *
47519 GTTTCCCTTGAAACAAATTTTATCTCCCTTGAGAT-A
1 GTTTCCCTTGAAACAAA---AATCT---TTGA-ATCT
47555 GTTTCCCTTGAAACAAAAATCTTTGAATCT
1 GTTTCCCTTGAAACAAAAATCTTTGAATCT
*
47585 GTTTCCCTTGAAACAAAAATCTTTGAATAT
1 GTTTCCCTTGAAACAAAAATCTTTGAATCT
47615 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
47632 CTTTGTCTCG
Statistics
Matches: 98, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
29 2 0.02
30 65 0.66
33 8 0.08
36 21 0.21
37 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (30 bp):
GTTTCCCTTGAAACAAAAATCTTTGAATCT
Found at i:47562 original size:66 final size:67
Alignment explanation
Indices: 47452--47601 Score: 239
Period size: 66 Copynumber: 2.3 Consensus size: 67
47442 CCTTGAGACA
* * * **
47452 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCAATCTTTGAAT
1 GTTTCCCTTGAAACAAAGTTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTGAAT
47517 CT
66 CT
*
47519 GTTTCCCTTGAAACAAA-TTTTATCTCCCTTGAGATAGTTTCCCTTGAAACAAAAATCTTTGAAT
1 GTTTCCCTTGAAACAAAGTTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTGAAT
47583 CT
66 CT
47585 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
47602 AATCTTTGAA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
66 61 0.79
67 16 0.21
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (67 bp):
GTTTCCCTTGAAACAAAGTTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAAATCTTTGAAT
CT
Found at i:47618 original size:96 final size:97
Alignment explanation
Indices: 47407--47669 Score: 307
Period size: 96 Copynumber: 2.6 Consensus size: 97
47397 TTTGTCTCCC
*
47407 TTGAGATA-GTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAGT
1 TTGA-ATATGTTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA--
** **
47471 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCAATCT
62 ----AATCTCTTGAGACAGTTTCCCTTGAAACAAAAATCT
* * *
47511 TTGAATCTGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGATAGTTTCCCTTGAAACAAAAATC
1 TTGAATATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAAATC
*
47576 T-TTGA-ATCTGTTTCCCTTGAAACAAAAATCT
66 TCTTGAGA-CAGTTTCCCTTGAAACAAAAATCT
* * *
47607 TTGAATATGTTTCCCTTGAAACAAACTTTGTCTCGCTTGAGACAGTTTTTCCTTGAAACAAAA
1 TTGAATATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG-TTTCCCTTGAAACAAAA
47670 TTTATCTCAC
Statistics
Matches: 141, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
95 1 0.01
96 65 0.46
97 19 0.13
103 35 0.25
104 21 0.15
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (97 bp):
TTGAATATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAAATC
TCTTGAGACAGTTTCCCTTGAAACAAAAATCT
Found at i:48149 original size:44 final size:44
Alignment explanation
Indices: 48084--48938 Score: 279
Period size: 44 Copynumber: 19.5 Consensus size: 44
48074 TCAACTTTTT
* * *
48084 GCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATATC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * **** *
48128 GTTCGATTCCATCACAGAAGGAGGTGGATCAACTTTTTTATTCC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * * * * * * * *
48172 GATCAAATCCAACGCATAAGGAGTTGGATCATA-ATC-AAATTTTT
1 GCTCGATTCCATCACAGAAGGAGGTAGATCA-ACATCGACA-TTTC
* * * * *
48216 GCTCGATTCTATCACAGAAGAAGGTTGATCAACACCGACATATC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
** * * * * ****
48260 ATTCAATTCCATCACATAAGGAGGTAGATTAATATTTTTATTTC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * * * * * * * * *
48304 GCTCAAATCCAACGCATAAGGAGTTGGATCAGCATCAACTTTTT
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* *
48348 GCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * * * ****
48392 GTTCGATTCCATCACGGAATGAAGTGGATCAACATTTTTATTTC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * * * * * * * *
48436 ACTCAAATCCAACGCATAAGGAGTTAGATCAACATCAACTTTTT
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * *
48480 GCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * ***
48524 GTTCGATTCCATCACGGAAGGAGGTGGATCAACAT--TTTTTTC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * ** * * * * * * * *
48566 ACTCAAATCCATCGTAGAATGAGTTGGATCAGCGTCAACTTTTT
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * *
48610 GCTCGATTCTATCACAG-AGTGATGTAGATCAGA-ATTGACATCTC
1 GCTCGATTCCATCACAGAAG-GAGGTAGATCA-ACATCGACATTTC
* ** * * * ****
48654 GTTCGATTCCATCGTAGAATGAGGTGGATCGACATTTTTATTTC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * * * * * * * *
48698 GCTCAAATCCATCGCATAAGGAGTTGGATCAGCATCAACTTTTT
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * *
48742 GCTAGATTCTATCACAGAATGAGGTAGAT-AAGCACCGACATTTC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAA-CATCGACATTTC
* * * * * ****
48786 GTTCGATTCCATCATAGAATGAGGTGGATCGACATTTTTATTTC
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * * * * * * *
48830 GCTCAAATCTATCGCATAAGGAGTTAGATCAACATCAACTTTTT
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
* * * * * * *
48874 TCTCAATTCTATCACAGAATGTGGTAGATCAGCA-CTGATATTAT-
1 GCTCGATTCCATCACAGAAGGAGGTAGATCAACATC-GACATT-TC
*
48918 GTTCGATTCCATCACAGAAGG
1 GCTCGATTCCATCACAGAAGG
48939 GGTTGGATCA
Statistics
Matches: 546, Mismatches: 251, Indels: 28
0.66 0.30 0.03
Matches are distributed among these distances:
42 27 0.05
43 6 0.01
44 507 0.93
45 6 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (44 bp):
GCTCGATTCCATCACAGAAGGAGGTAGATCAACATCGACATTTC
Found at i:48316 original size:132 final size:132
Alignment explanation
Indices: 48074--48960 Score: 1099
Period size: 132 Copynumber: 6.7 Consensus size: 132
48064 AATAAATTGT
*
48074 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATATCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
* * * *
48139 TCACAGAAGGAGGTGGATCAACTTTTTTATTCCGATCAAATCCAACGCATAAGGAGTTGGATCAT
66 TCACAGAAGGAGGTGGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATCAG
48204 AA
131 AA
* * * * * *
48206 TCAAATTTTTGCTCGATTCTATCACAGAAGAAGGTTGATCAACACCGACATATCATTCAATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
* * * *
48271 TCACATAAGGAGGTAGATTAATATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATCAG
66 TCACAGAAGGAGGTGGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATCAG
*
48336 CA
131 AA
*
48338 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
* * * * *
48403 TCACGGAATGAAGTGGATCAACATTTTTATTTCACTCAAATCCAACGCATAAGGAGTTAGATCA-
66 TCACAGAAGGAGGTGGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATCAG
48467 ACA
131 A-A
* * *
48470 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
* * * * * *
48535 TCACGGAAGGAGGTGGATCAACA-TTTT-TTTCACTCAAATCCATCGTAGAATGAGTTGGATCAG
66 TCACAGAAGGAGGTGGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATCAG
**
48598 CG
131 AA
* **
48600 TCAACTTTTTGCTCGATTCTATCACAG-AGTGATGTAGATCAGA-ATTGACATCTCGTTCGATTC
1 TCAACTTTTTGCTCGATTCTATCACAGAAG-GAGGTAGATCA-ACACCGACATCTCGTTCGATTC
** * * *
48663 CATCGTAGAATGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCATAAGGAGTTGGATC
64 CATCACAGAAGGAGGTGGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATC
*
48728 AGCA
129 AGAA
* * *
48732 TCAACTTTTTGCTAGATTCTATCACAGAATGAGGTAGAT-AAGCACCGACATTTCGTTCGATTCC
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAA-CACCGACATCTCGTTCGATTCC
* * * * * *
48796 ATCATAGAATGAGGTGGATCGACATTTTTATTTCGCTCAAATCTATCGCATAAGGAGTTAGATCA
65 ATCACAGAAGGAGGTGGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATCA
48861 -ACA
130 GA-A
* * * * * * * *
48864 TCAACTTTTTTCTCAATTCTATCACAGAATGTGGTAGATCAGCACTGATAT-TATGTTCGATTCC
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCT-CGTTCGATTCC
* *
48928 ATCACAGAAGG-GGTTGGATCAATATTTTCATTT
65 ATCACAGAAGGAGG-TGGATCAACATTTTTATTT
48961 TTGCTAGATT
Statistics
Matches: 663, Mismatches: 79, Indels: 26
0.86 0.10 0.03
Matches are distributed among these distances:
129 1 0.00
130 107 0.16
131 12 0.02
132 541 0.82
133 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (132 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATCAG
AA
Found at i:48815 original size:394 final size:393
Alignment explanation
Indices: 48074--48955 Score: 1191
Period size: 394 Copynumber: 2.2 Consensus size: 393
48064 AATAAATTGT
* *
48074 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATATCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCA-CGACAT-TCGTTCGATTCCA
* * *
48139 TCACAGAAGGAGGTGGATCAACTTTTTTATTCCGATCAAATCCAACGCATAAGGAGTTGGATCAT
64 TCACAGAAGGAGGTGGATCAACATTTTTATTCC-ATCAAATCCAACGCAGAAGGAGTTGGATCAG
*
48204 AATCAAATTTTTGCTCGATTCTATCACAGAAGAAGGTTGATCAACACCGACATATCATTCAATTC
128 AATCAAATTTTTGCTCGATTCTATCACAGAAGAAGGTAGATCAACACCGACATATCATTCAATTC
* * *
48269 CATCACATAAGGAGGTAGATTAATATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATC
193 CATCACAGAAGGAGGTAGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATC
* *
48334 AGCATCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCGAT
258 AGCATCAACTTTTTGCTAGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGAT
*
48399 TCCATCACGGAATGAAGTGGATCAACATTTTTATTTCACTCAAATCCAACGCATAAGGAGTTAGA
323 TCCATCACAGAATGAAGTGGATCAACATTTTTATTTCACTCAAATCCAACGCATAAGGAGTTAGA
48464 TCAACA
388 TCAACA
48470 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCA-CGACAT-TCGTTCGATTCCA
* * * *
48535 TCACGGAAGGAGGTGGATCAACATTTTT-TT-CACTCAAATCCATCGTAGAATGAGTTGGATCAG
64 TCACAGAAGGAGGTGGATCAACATTTTTATTCCA-TCAAATCCAACGCAGAAGGAGTTGGATCAG
** * * * ** * * *
48598 CGTCAACTTTTTGCTCGATTCTATCACAG-AGTGATGTAGATCAGA-ATTGACATCTCGTTCGAT
128 AATCAAATTTTTGCTCGATTCTATCACAGAAG-AAGGTAGATCA-ACACCGACATATCATTCAAT
** * * * *
48661 TCCATCGTAGAATGAGGTGGATCGACATTTTTATTTCGCTCAAATCCATCGCATAAGGAGTTGGA
191 TCCATCACAGAAGGAGGTAGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGA
* *
48726 TCAGCATCAACTTTTTGCTAGATTCTATCACAGAATGAGGTAGAT-AAGCACCGACATTTCGTTC
256 TCAGCATCAACTTTTTGCTAGATTCTATCACAGAAGGAGGTAGATCAA-CACCGACATCTCGTTC
* * * * * *
48790 GATTCCATCATAGAATGAGGTGGATCGACATTTTTATTTCGCTCAAATCTATCGCATAAGGAGTT
320 GATTCCATCACAGAATGAAGTGGATCAACATTTTTATTTCACTCAAATCCAACGCATAAGGAGTT
48855 AGATCAACA
385 AGATCAACA
* * * * * *
48864 TCAACTTTTTTCTCAATTCTATCACAGAATGTGGTAGATCAGCACTGATATTATGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCAC-GACATT-CGTTCGATTCCA
*
48929 TCACAGAAGG-GGTTGGATCAATATTTT
64 TCACAGAAGGAGG-TGGATCAACATTTT
48956 CATTTTTGCT
Statistics
Matches: 429, Mismatches: 50, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
393 9 0.02
394 330 0.77
395 3 0.01
396 87 0.20
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (393 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAAGAGGTAGATCAGCACGACATTCGTTCGATTCCATC
ACAGAAGGAGGTGGATCAACATTTTTATTCCATCAAATCCAACGCAGAAGGAGTTGGATCAGAAT
CAAATTTTTGCTCGATTCTATCACAGAAGAAGGTAGATCAACACCGACATATCATTCAATTCCAT
CACAGAAGGAGGTAGATCAACATTTTTATTTCGCTCAAATCCAACGCATAAGGAGTTGGATCAGC
ATCAACTTTTTGCTAGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCC
ATCACAGAATGAAGTGGATCAACATTTTTATTTCACTCAAATCCAACGCATAAGGAGTTAGATCA
ACA
Found at i:51231 original size:31 final size:28
Alignment explanation
Indices: 51172--51233 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 28
51162 TTTTATGTTG
**
51172 TTTTACTATTTTATTTTTTATTTGTTGT
1 TTTTACTATTTTATTTTTTATTAATTGT
*
51200 TTTTATTATTTTAATTATGTTTATTAATTGT
1 TTTTACTATTTT-ATT-T-TTTATTAATTGT
51231 TTT
1 TTT
51234 AATGCTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.39
29 3 0.11
30 1 0.04
31 13 0.46
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (28 bp):
TTTTACTATTTTATTTTTTATTAATTGT
Found at i:53976 original size:21 final size:20
Alignment explanation
Indices: 53950--53989 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53940 GATTCACAAA
53950 AATATTATTACCAGAAAAAAT
1 AATATT-TTACCAGAAAAAAT
* *
53971 AATATTTTTCGAGAAAAAA
1 AATATTTTACCAGAAAAAA
53990 AAACTTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (20 bp):
AATATTTTACCAGAAAAAAT
Found at i:54390 original size:2 final size:2
Alignment explanation
Indices: 54385--54676 Score: 144
Period size: 2 Copynumber: 151.5 Consensus size: 2
54375 TTTTTTATTT
*
54385 TA TA TA TA TG TA TA GTA TA TA T- TA TA TGA TA TA T- TA T- TA T-
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
* *
54425 TA TA T- TA -A TA TA TA -A TA TA TA TG TA GTA TA TA T- TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
54464 T- TA TA TA GTG TA TA TA TA TT TA GTA TA T- TT TA TA TA TA T- TA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
54505 TA TT TA T- TA TA TA GTA TA TT TA GTA TA TA T- TA TA CTA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * *
54546 TA TA T- TC TA TA GTA TA GTA TA TA TA T- TG TA TA TG T- TA TA TT
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
54587 TA T- TA T- TA TA TT TA TA TA T- TA TA -A TA TA AA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
54625 TA CTA TA TT TA TA TT TA TA TA T- TA TT TA GTG TA TA TA TA TA T-
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
54667 TA TA T- TA TA T
1 TA TA TA TA TA T
54677 TAATGTTATT
Statistics
Matches: 221, Mismatches: 34, Indels: 70
0.68 0.10 0.22
Matches are distributed among these distances:
1 23 0.10
2 176 0.80
3 22 0.10
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.54
Consensus pattern (2 bp):
TA
Found at i:54427 original size:6 final size:5
Alignment explanation
Indices: 54379--54735 Score: 120
Period size: 5 Copynumber: 71.4 Consensus size: 5
54369 CAACCCTTTT
*
54379 TTATT TTATA -TATA TGTATA GTATATA TTATA TGATATA TTATTA TTATA
1 TTATA TTATA TTATA T-TATA -T-TATA TTATA T--TATA TTA-TA TTATA
*
54429 TTA-A -TATA TAATA -TATA TGTAGTA -TATA TTAT- TTAT- TATATA
1 TTATA TTATA TTATA TTATA T-TA-TA TTATA TTATA TTATA T-TATA
* *
54471 GTGTATA -TATA TT-TA GTATA TTTTA TATATA TTATA TT-TA TTATA
1 -T-TATA TTATA TTATA TTATA TTATA T-TATA TTATA TTATA TTATA
* * *
54516 TAGTATA TT-TA GTATATA TTATA CTATA TATATA TTCTATA GTATA GTATA
1 T--TATA TTATA -T-TATA TTATA TTATA T-TATA -T-TATA TTATA TTATA
* * *
54567 -TATA TTGTA -TATG TTATA TTTATTA TTATA TT-TA -TATA TTATA ATATA
1 TTATA TTATA TTATA TTATA -TTA-TA TTATA TTATA TTATA TTATA TTATA
* * *
54615 -AATA -TATA TT-TA CTATA TTTATA TT-TA -TATA TTAT- TTAGT- GTATA
1 TTATA TTATA TTATA TTATA -TTATA TTATA TTATA TTATA TTA-TA TTATA
* * **
54660 TATATA TTATA TTATA TTAATG TTAT- TTATT TTACC TTATA TTTATA
1 T-TATA TTATA TTATA TT-ATA TTATA TTATA TTATA TTATA -TTATA
*
54707 TTTATA TT-TA TTA-A TT-TA TT-TA TTTTA TT
1 -TTATA TTATA TTATA TTATA TTATA TTATA TT
54736 TCAGGTCCAA
Statistics
Matches: 277, Mismatches: 29, Indels: 92
0.70 0.07 0.23
Matches are distributed among these distances:
3 4 0.01
4 74 0.27
5 116 0.42
6 52 0.19
7 31 0.11
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:54701 original size:41 final size:40
Alignment explanation
Indices: 54656--54733 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 40
54646 TTATTTAGTG
54656 TATATATATA-TTATATTATATTAATGTTATTTATTTTACCT
1 TATATATATATTTATATT-TATTAAT-TTATTTATTTTACCT
*
54697 TATATTTATATTTATATTTATTAATTTATTTATTTTA
1 TATATATATATTTATATTTATTAATTTATTTATTTTA
54734 TTTCAGGTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 12 0.34
41 16 0.46
42 7 0.20
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (40 bp):
TATATATATATTTATATTTATTAATTTATTTATTTTACCT
Found at i:55865 original size:35 final size:33
Alignment explanation
Indices: 55826--55895 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 33
55816 GTTTAACCCT
*
55826 TTTAATTTGAATTTCTTTTTATTTCT-TTTTATTTA
1 TTTAATTTGAATTT-ATTTTATTT-TATTTT-TTTA
*
55861 TTTAATTTTAATTTATTTTATTTTATTTTTTTA
1 TTTAATTTGAATTTATTTTATTTTATTTTTTTA
55894 TT
1 TT
55896 ATAACCCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 7 0.22
34 12 0.38
35 13 0.41
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.74
Consensus pattern (33 bp):
TTTAATTTGAATTTATTTTATTTTATTTTTTTA
Found at i:55886 original size:5 final size:5
Alignment explanation
Indices: 55842--55889 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
55832 TTGAATTTCT
* *
55842 TTTTA TTTCT- TTTTA -TTTA TTTAA TTTTA ATTTA TTTTA TTTTA TTTT
1 TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
55890 TTTATTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 5 0.14
5 30 0.83
6 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Done.