Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_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: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 21
Found at i:575721 original size:86 final size:85
Alignment explanation
Indices: 575572--575964 Score: 303
Period size: 86 Copynumber: 4.6 Consensus size: 85
575562 ACAAAAAATT
* * * * *
575572 CCACAATAGGTGTTGATATTTAGTGGCGTTTG-AACAAAAAATGCCGTAATAAGTGTTGATATTT
1 CCACAATAGGTTTTGATATTTAGCGGCGTTTGTAA-TAAAAACGCCGCAAT-AGTGTTGATATTT
575636 AGCAGAGTTTATATAACAAACG
64 AGCAGAGTTTATATAACAAACG
** *
575658 CCGTAATAGGTTTTGATATTTAAG-GGCGTTTGTATTAAAAACGCCGCAATAGTTGTTGATATTT
1 CCACAATAGGTTTTGATATTT-AGCGGCGTTTGTAATAAAAACGCCGCAATAG-TGTTGATATTT
* * * * *
575722 AACGGTGTTTGTATTACAAACG
64 AGCAGAGTTTATATAACAAACG
*
575744 CCACAATAGGTTTTGATATTTAGCGGCGTTTGTAATAAAAACGCCGCAATAGATGTTGATGTTTA
1 CCACAATAGGTTTTGATATTTAGCGGCGTTTGTAATAAAAACGCCGCAATAG-TGTTGATATTTA
* * * * *
575809 GCGGCGTTTTTTTCACAAACG
65 GCAGAGTTTATATAACAAACG
* * * * * ** ** *
575830 CCGCAGT-GGTTATTGAGATTTAGCGGTGTTT-TTATCGCAAACGTTGCAATAAGTGTTGAAATT
1 CCACAATAGGTT-TTGATATTTAGCGGCGTTTGTAAT-AAAAACGCCGCAAT-AGTGTTGATATT
* ***
575893 TAGCGGCA-TTT-TCCCACAAACG
63 TAGCAG-AGTTTATATAACAAACG
* * ** * *
575915 CCGCAATAGGTGTTGAGCTTTAGCGGCGTTTGTTCATACAAACGCCGCAA
1 CCACAATAGGTTTTGATATTTAGCGGCGTTTG-TAATAAAAACGCCGCAA
575965 AAAGATCGCT
Statistics
Matches: 252, Mismatches: 44, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
85 43 0.17
86 201 0.80
87 8 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (85 bp):
CCACAATAGGTTTTGATATTTAGCGGCGTTTGTAATAAAAACGCCGCAATAGTGTTGATATTTAG
CAGAGTTTATATAACAAACG
Found at i:575795 original size:129 final size:129
Alignment explanation
Indices: 575627--575964 Score: 301
Period size: 129 Copynumber: 2.6 Consensus size: 129
575617 GTAATAAGTG
* * *
575627 TTGATATTTAGCAGAGTTTATATAACAAACGCCGTAATAGGTTTTGATATTTAAG-GGCGTTTGT
1 TTGATATTTAGCAGAGTTTATATAACAAACGCCGCAATAGATGTTGATATTT-AGCGGCGTTT-T
* *
575691 ATT-AAAAACGCCGCAATAGTTGTTGATATTTAACGGTGTTTGTATTACAAACGCCACAATAGGT
64 ATTCAAAAACGCCGCAATAGTTATTGAGATTTAACGGTGTTTGTATTACAAACGCCACAATAGGT
575755 T
129 T
* * * * *
575756 TTGATATTTAGCGGCGTTTGTAATAA-AAACGCCGCAATAGATGTTGATGTTTAGCGGCGTTTTT
1 TTGATATTTAGCAGAGTTTAT-ATAACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTA
* * * * * ** *** * *
575820 TTCACAAACGCCGCAGTGGTTATTGAGATTTAGCGGTGTTTTTATCGCAAACGTTGCAATAAGTG
65 TTCAAAAACGCCGCAATAGTTATTGAGATTTAACGGTGTTTGTATTACAAACGCCACAATAGGTT
* * *** * ** *
575885 TTGAAATTTAGCGGCA-TTT-TCCCACAAACGCCGCAATAGGTGTTGAGCTTTAGCGGCG-TTTG
1 TTGATATTTAGCAG-AGTTTATATAACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTA
575947 TTCATACAAACGCCGCAA
65 TTCA-A-AAACGCCGCAA
575965 AAAGATCGCT
Statistics
Matches: 169, Mismatches: 33, Indels: 14
0.78 0.15 0.06
Matches are distributed among these distances:
127 8 0.05
128 36 0.21
129 121 0.72
130 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (129 bp):
TTGATATTTAGCAGAGTTTATATAACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTAT
TCAAAAACGCCGCAATAGTTATTGAGATTTAACGGTGTTTGTATTACAAACGCCACAATAGGTT
Found at i:575998 original size:44 final size:42
Alignment explanation
Indices: 575935--576048 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 42
575925 TGTTGAGCTT
** *
575935 TAGCGGCGTTTGTTCATACAAACGCCGCAAAAAGATCGCTATA
1 TAGCGGCGTTT-TAGATACAAACGCCGCAAAAAGACCGCTATA
* * *
575978 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAGATACCGCTATA
1 TAGCGGCG-TTTTA-GATACAAACGCCGCAAAAAGACCGCTATA
* *
576022 TTGCGGTGTTTTAGATACAAACGCCGC
1 TAGCGGCGTTTTAGATACAAACGCCGC
576049 TAAATGTTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 14 0.23
43 14 0.23
44 33 0.54
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTTAGATACAAACGCCGCAAAAAGACCGCTATA
Found at i:576064 original size:42 final size:42
Alignment explanation
Indices: 575950--576096 Score: 145
Period size: 44 Copynumber: 3.4 Consensus size: 42
575940 GCGTTTGTTC
* * * *
575950 ATACAAACGCCGCAAAAAGATCGCTATATAGCGGCGTTTTTAGG
1 ATACAAACGCCGCTAAATGATCGCTATATTGCGGTG-TTTTA-G
*
575994 ATACAAACGCCGCTAAGAT-ACCGCTATATTGCGGTGTTTTAG
1 ATACAAACGCCGCTAA-ATGATCGCTATATTGCGGTGTTTTAG
* * * *
576036 ATACAAACGCCGCTAAATGTTTGATATATTGCGGCAT-TTTTTG
1 ATACAAACGCCGCTAAATGATCGCTATATTGCGG--TGTTTTAG
*
576079 TTACAAACGCCGCTAAAT
1 ATACAAACGCCGCTAAAT
576097 AACTAAGAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
41 2 0.02
42 28 0.32
43 27 0.31
44 30 0.34
45 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (42 bp):
ATACAAACGCCGCTAAATGATCGCTATATTGCGGTGTTTTAG
Found at i:576435 original size:21 final size:21
Alignment explanation
Indices: 576411--576456 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
576401 GCTGATATGT
* *
576411 TGCTTATCTTTGTGCTTTCGC
1 TGCTTATCTATGTGCTTCCGC
*
576432 TGCTTCTCTATGTGCTTCCGC
1 TGCTTATCTATGTGCTTCCGC
576453 TGCT
1 TGCT
576457 GTTCTCTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.28, G:0.20, T:0.48
Consensus pattern (21 bp):
TGCTTATCTATGTGCTTCCGC
Found at i:584954 original size:42 final size:42
Alignment explanation
Indices: 584489--584948 Score: 591
Period size: 42 Copynumber: 11.0 Consensus size: 42
584479 TATTATGACA
* * * * *
584489 TTTGAACTATAAATGCCGCTATAATACTACTATATTGTGGCG
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
** * * * *
584531 TTTCTTG-TA-AAACTCCGCTATATTACTACTATATTGTGGCA
1 TTT-GAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
*
584572 TTTGAGCTATAAACGCCGCTATATTACGACTCTATTGCGGCG
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
* * * **
584614 TTTGAGCTATAAATGCTGATATATTACTACTCTATTATGGCG
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
*
584656 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCAGCG
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
* * * **
584698 TTTGTGCTATAAACGACGCTATATTACAACTCTATTATGGCG
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
*
584740 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTACGGCG
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
*
584782 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTACGGCG
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
* *
584824 TTTGAGCTATAAACGCTGCTATATTACGACTCTATTGCGGCG
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
* * *
584866 TTTGAGCTATAAATGCCGCTATATTACTACTCTATTTCGACG
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
** * *
584908 TTTTTGCTATAAACGCCACTATATTACTACTCAATTGCGGC
1 TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGC
584949 ATTTTTACAA
Statistics
Matches: 364, Mismatches: 51, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
40 1 0.00
41 33 0.09
42 330 0.91
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (42 bp):
TTTGAGCTATAAACGCCGCTATATTACTACTCTATTGCGGCG
Found at i:586517 original size:83 final size:82
Alignment explanation
Indices: 586393--586568 Score: 191
Period size: 83 Copynumber: 2.1 Consensus size: 82
586383 GTACATGTTT
* * *
586393 TTGCAGCGTTTTTA-TA-AAAGCGCCACTATAGACAAACATATTGCGT-CGTTTGTAGGGA-AAA
1 TTGCAGCGTTTTTAGCACAAA-CGCCACTATAAACAAACATATT-C-TACGTTT-TAGCGATAAA
**
586454 CGCCACTAAATTATTACTCTA
62 CGCCACTAAATTACCACTCTA
* *
586475 TTGCGGCGTTTTTAGCACAAACGCCACTATAAAC-AACTATATTCTAGCGTTTTAGCTATAAACG
1 TTGCAGCGTTTTTAGCACAAACGCCACTATAAACAAAC-ATATTCTA-CGTTTTAGCGATAAACG
*
586539 CCGCTAAATTACCACTCTA
64 CCACTAAATTACCACTCTA
586558 TTGCAGCGTTT
1 TTGCAGCGTTT
586569 GTTGAAAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
81 1 0.01
82 21 0.27
83 54 0.68
84 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (82 bp):
TTGCAGCGTTTTTAGCACAAACGCCACTATAAACAAACATATTCTACGTTTTAGCGATAAACGCC
ACTAAATTACCACTCTA
Found at i:586568 original size:42 final size:41
Alignment explanation
Indices: 586451--586568 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 41
586441 TTTGTAGGGA
** *
586451 AAACGCCACTAAATTATTACTCTATTGCGGCGTTTTTAGCAC
1 AAACGCCACTAAATTACAACTCTATTGCAGCG-TTTTAGCAC
* *
586493 AAACGCCACTATAA--ACAACTATATT-CTAGCGTTTTAGCTAT
1 AAACGCCACTA-AATTACAACTCTATTGC-AGCGTTTTAGC-AC
* *
586534 AAACGCCGCTAAATTACCACTCTATTGCAGCGTTT
1 AAACGCCACTAAATTACAACTCTATTGCAGCGTTT
586569 GTTGAAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
40 10 0.16
41 22 0.35
42 27 0.44
43 3 0.05
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (41 bp):
AAACGCCACTAAATTACAACTCTATTGCAGCGTTTTAGCAC
Found at i:589174 original size:16 final size:16
Alignment explanation
Indices: 589153--589186 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
589143 TTACTATTCA
*
589153 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
589169 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
589185 CG
1 CG
589187 ATCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:594345 original size:39 final size:36
Alignment explanation
Indices: 594268--594516 Score: 191
Period size: 38 Copynumber: 6.4 Consensus size: 36
594258 TATTTTTGAA
* *
594268 AAAAATATAATATATAGTTTTTAGAAAATGGTTCTTG
1 AAAAATATAATATATAATTTTTAAAAAATGGTT-TTG
594305 AAAGAATATAATATATAATTTTTAAAAAATCGGGTTTTG
1 AAA-AATATAATATATAATTTTTAAAAAAT--GGTTTTG
* *
594344 -AAAATATATATATATAATATGGTTTTGAAAACATGTTTTTG
1 AAAAATATA-ATATAT-A-AT--TTTT-AAAAAATGGTTTTG
* * **
594385 AAAACATATAATATATAGTTTTGAAAAAATATTTTTG
1 AAAA-ATATAATATATAATTTTTAAAAAATGGTTTTG
* *
594422 AAAACGTATATAATATATAGTTTTTTAAAAATCGGTTTTGG
1 AAAA---ATATAATATATAATTTTTAAAAAAT-GGTTTT-G
594463 AAAACATATAATATAT-ATTTTTGAAAACACAT--TTTTG
1 AAAA-ATATAATATATAATTTTT-AAAA-A-ATGGTTTTG
594500 AAAATATATAATATATA
1 AAAA-ATATAATATATA
594517 GTTTGAAAAT
Statistics
Matches: 176, Mismatches: 17, Indels: 37
0.77 0.07 0.16
Matches are distributed among these distances:
37 41 0.23
38 44 0.25
39 41 0.23
40 12 0.07
41 14 0.08
42 13 0.07
43 11 0.06
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (36 bp):
AAAAATATAATATATAATTTTTAAAAAATGGTTTTG
Found at i:594406 original size:37 final size:36
Alignment explanation
Indices: 594243--594568 Score: 248
Period size: 39 Copynumber: 8.5 Consensus size: 36
594233 ATTAATATAG
*
594243 TATAGATTTTG-AAAATATTTTTGAAAAAAATATAATA
1 TATAG-TTTTGAAAAATATTTTTG-AAAACATATAATA
* * *
594280 TATAGTTTTTAGAAAATGGTTCTTGAAAGA-ATATAATA
1 TATAGTTTTGA-AAAAT-ATTTTTGAAA-ACATATAATA
* * *
594318 TATAATTTTTAAAAA-ATCGGGTTTTGAAAATATATATATA
1 TATAGTTTTGAAAAATAT----TTTTGAAAACATATA-ATA
*
594358 TAATATGGTTTTGAAAACATGTTTTTGAAAACATATAATA
1 T-ATA--GTTTTGAAAA-ATATTTTTGAAAACATATAATA
594398 TATAGTTTTGAAAAAATATTTTTGAAAACGTATATAATA
1 TATAGTTTTG-AAAAATATTTTTGAAAAC--ATATAATA
* * *
594437 TATAGTTTTTTAAAAATCGGTTTTGGAAAACATATAATA
1 TATAG-TTTTGAAAAAT--ATTTTTGAAAACATATAATA
* * *
594476 TATATTTTTGAAAACACATTTTTGAAAATATATAATA
1 TATAGTTTTGAAAA-ATATTTTTGAAAACATATAATA
**
594513 TATAG-TTTG-AAAATATTTTTGAAAATGTATATATAA
1 TATAGTTTTGAAAAATATTTTTGAAAACATATA-AT-A
594549 TATAGTTTTTGAAAACATAT
1 TATAG-TTTTGAAAA-ATAT
594569 AATATATAGT
Statistics
Matches: 238, Mismatches: 23, Indels: 53
0.76 0.07 0.17
Matches are distributed among these distances:
34 17 0.07
35 6 0.03
36 14 0.06
37 49 0.21
38 43 0.18
39 56 0.24
40 16 0.07
41 27 0.11
43 8 0.03
44 1 0.00
45 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (36 bp):
TATAGTTTTGAAAAATATTTTTGAAAACATATAATA
Found at i:594422 original size:78 final size:75
Alignment explanation
Indices: 594254--594568 Score: 293
Period size: 78 Copynumber: 4.1 Consensus size: 75
594244 ATAGATTTTG
* * *
594254 AAAATATTTTTGAAAAAAATATAATATATA-GTTTTTAGAAAATGGTTCTTGAAAGA-ATATAAT
1 AAAATATTTTTG-AAAATATATAATATATAGGTTTTGA-AAAATGGTTTTTGAAA-ACATATAAT
* *
594317 ATATAATTTTTAA
63 ATATAGTTTTGAA
**
594330 AAAATCGGGTTTTGAAAATATATATATATAATATGGTTTTGAAAACAT-GTTTTTGAAAACATAT
1 AAAAT--ATTTTTGAAAATATATA-ATAT-ATA-GGTTTTGAAAA-ATGGTTTTTGAAAACATAT
594394 AATATATAGTTTTGAA
60 AATATATAGTTTTGAA
* * *
594410 AAAATATTTTTGAAAACGTATATAATATATAGTTTTTTAAAAATCGGTTTTGGAAAACATATAAT
1 AAAATATTTTTGAAAA--TATATAATATATAGGTTTTGAAAAAT-GGTTTTTGAAAACATATAAT
*
594475 ATATATTTTTGAA
63 ATATAGTTTTGAA
* * * **
594488 AACACATTTTTGAAAATATATAATATATA-G-TTTG-AAAAT-ATTTTTGAAAATGTATATATAA
1 AAAATATTTTTGAAAATATATAATATATAGGTTTTGAAAAATGGTTTTTGAAAACATATA-AT-A
594549 TATAGTTTTTGAA
64 TATAG-TTTTGAA
*
594562 AACATAT
1 AAAATAT
594569 AATATATAGT
Statistics
Matches: 201, Mismatches: 23, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
71 13 0.06
72 2 0.01
73 10 0.05
74 16 0.08
76 20 0.10
77 18 0.09
78 65 0.32
79 8 0.04
80 41 0.20
81 8 0.04
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.41
Consensus pattern (75 bp):
AAAATATTTTTGAAAATATATAATATATAGGTTTTGAAAAATGGTTTTTGAAAACATATAATATA
TAGTTTTGAA
Found at i:594583 original size:26 final size:26
Alignment explanation
Indices: 594528--594582 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
594518 TTTGAAAATA
**
594528 TTTTTGAAAATGTATATATAATATAG
1 TTTTTGAAAACATATATATAATATAG
594554 TTTTTGAAAACATATA-AT-ATATAG
1 TTTTTGAAAACATATATATAATATAG
594578 TTTTT
1 TTTTT
594583 TAAATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 11 0.41
25 2 0.07
26 14 0.52
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (26 bp):
TTTTTGAAAACATATATATAATATAG
Found at i:594597 original size:35 final size:35
Alignment explanation
Indices: 594555--594622 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
594545 ATAATATAGT
* *
594555 TTTTGAAAACATATAATATATAGTTTTTTAAATAA
1 TTTTGAAAACATATAATATATAATTTTTAAAATAA
**
594590 TTTTGAAAACATATTGTATATAATTTTTAAAAT
1 TTTTGAAAACATATAATATATAATTTTTAAAAT
594623 GGTTTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (35 bp):
TTTTGAAAACATATAATATATAATTTTTAAAATAA
Found at i:594629 original size:97 final size:97
Alignment explanation
Indices: 594456--594635 Score: 231
Period size: 97 Copynumber: 1.9 Consensus size: 97
594446 TTAAAAATCG
*
594456 GTTTTGGAAAACATATAATATATATTTTTGAAAACACATTTTTGAAAATATATAATATATAGTTT
1 GTTTTGGAAAACATATAATATATATTTTTGAAAACACATTTTTGAAAACATATAATATATAGTTT
594521 GAAAATATTTTTGAAAATGTATATATAATATA
66 GAAAATATTTTTGAAAATGTATATATAATATA
* * * ** *
594553 GTTTTTGAAAACATATAATATATAGTTTTT-TAAATA-A-TTTTGAAAACATATTGTATATAATT
1 GTTTTGGAAAACATATAATATATA-TTTTTGAAAACACATTTTTGAAAACATATAATATAT-AGT
* *
594615 TTTAAAATGGTTTTTGAAAAT
64 TTGAAAAT-ATTTTTGAAAAT
594636 ATAATGTATG
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 18 0.25
96 10 0.14
97 38 0.54
98 5 0.07
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.44
Consensus pattern (97 bp):
GTTTTGGAAAACATATAATATATATTTTTGAAAACACATTTTTGAAAACATATAATATATAGTTT
GAAAATATTTTTGAAAATGTATATATAATATA
Found at i:594700 original size:14 final size:16
Alignment explanation
Indices: 594677--594732 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 16
594667 TATAGTATAC
594677 ATATTATATATATTATT
1 ATATTATATAT-TTATT
594694 -TATTATATATTTATT
1 ATATTATATATTTATT
594709 ATATTATAT-TGTTATT
1 ATATTATATAT-TTATT
594725 AATATTAT
1 -ATATTAT
594733 TTTTCATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.17
16 23 0.64
17 7 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
ATATTATATATTTATT
Found at i:599383 original size:2 final size:2
Alignment explanation
Indices: 599376--599401 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
599366 GGGTTTTTGA
599376 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
599402 GGTTTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:599424 original size:25 final size:24
Alignment explanation
Indices: 599391--599436 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
599381 TATATATATA
*
599391 TATATATATATGGTTTTGAAAACG
1 TATATATATATAGTTTTGAAAACG
599415 TATA-ATATATAGTTTTGAAAAC
1 TATATATATATAGTTTTGAAAAC
599437 ATATTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (24 bp):
TATATATATATAGTTTTGAAAACG
Found at i:599519 original size:28 final size:26
Alignment explanation
Indices: 599498--599551 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
599488 ATATAGTTTT
599498 TAAAAT-ATTTTTGAAAACATATATA
1 TAAAATAATTTTTGAAAACATATATA
*
599523 TAATATAATTTTTGAAAACATATAATA
1 TAAAATAATTTTTGAAAACATAT-ATA
599550 TA
1 TA
599552 TAGATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 5 0.19
26 16 0.62
27 5 0.19
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
TAAAATAATTTTTGAAAACATATATA
Found at i:599552 original size:24 final size:27
Alignment explanation
Indices: 599504--599560 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
599494 TTTTTAAAAT
599504 ATTTTTGAAAACATATATATAATATA-
1 ATTTTTGAAAACATATATATAATATAG
599530 ATTTTTGAAAACATATA-AT-ATATAG
1 ATTTTTGAAAACATATATATAATATAG
599555 ATTTTT
1 ATTTTT
599561 TTAAATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 5 0.17
25 8 0.27
26 17 0.57
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (27 bp):
ATTTTTGAAAACATATATATAATATAG
Found at i:599561 original size:63 final size:64
Alignment explanation
Indices: 599333--599590 Score: 222
Period size: 65 Copynumber: 3.9 Consensus size: 64
599323 AAAATGGTTC
* *
599333 TTAAAAGCATATAATATATAG-TTTTTTAAAAATGGGTTTTTGAATATATATATATATATATATA
1 TTAAAA-CATATAATATATAGATTTTTT-AAAAT--ATTTTTG-A-A-A-ACATATATATATATA
599397 TATATGGTT
58 TA-AT-GTT
* ** * * *
599406 TTGAAAACGTATAATATATAG-TTTTGAAAACATATTTTTGAAAACGTATATA-ATATATAGTAT
1 TT-AAAACATATAATATATAGATTTTTTAAA-ATATTTTTGAAAACATATATATATATATAATGT
599469 T
64 T
* *
599470 TTAAAA-ATTATATATAATATATAGTTTTTAAAATATTTTTGAAAACATATATATA-ATATAAT-
1 TTAAAACA-TATA-AT-ATATAGATTTTTTAAAATATTTTTGAAAACATATATATATATATAATG
599532 TT
63 TT
*
599534 TTGAAAACATATAATATATAGATTTTTTTAAATATTTTTGAAAACATATAGTATATA
1 TT-AAAACATATAATATATAGATTTTTTAAAATATTTTTGAAAACATATA-TATATA
599591 ATTTTTAAAA
Statistics
Matches: 156, Mismatches: 18, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
63 40 0.26
64 16 0.10
65 41 0.26
66 15 0.10
67 7 0.04
68 1 0.01
69 1 0.01
70 1 0.01
71 6 0.04
72 3 0.02
73 21 0.13
74 4 0.03
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (64 bp):
TTAAAACATATAATATATAGATTTTTTAAAATATTTTTGAAAACATATATATATATATAATGTT
Found at i:599616 original size:63 final size:63
Alignment explanation
Indices: 599384--599600 Score: 194
Period size: 63 Copynumber: 3.4 Consensus size: 63
599374 GAATATATAT
* * *
599384 ATATATATATATATATATGGTTTTGAAAACGTAT--AATATATAGTTTTGAAAACATATTTTTGA
1 ATATATATA-ATATA-AT--TTTTGAAAACATATAAAATATAGAGTTTT-TAAA-ATATTTTTGA
599447 AAAC
60 AAAC
* * * * * *
599451 GTATATA-ATATATAGTATTTTAAAAATTATATATAATATATAGTTTTTAAAATATTTTTGAAAA
1 ATATATATA-ATATAAT-TTTTGAAAA-CATATAAAATATAGAGTTTTTAAAATATTTTTGAAAA
599515 C
63 C
* * *
599516 ATATATATAATATAATTTTTGAAAACATATAATATATAGATTTTTTTAAATATTTTTGAAAAC
1 ATATATATAATATAATTTTTGAAAACATATAAAATATAGAGTTTTTAAAATATTTTTGAAAAC
*
599579 ATATA-GT-ATATAATTTTT-AAAA
1 ATATATATAATATAATTTTTGAAAA
599601 TGGTTTTGAA
Statistics
Matches: 129, Mismatches: 17, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
60 4 0.03
61 11 0.09
62 1 0.01
63 37 0.29
64 16 0.12
65 30 0.23
66 11 0.09
67 19 0.15
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (63 bp):
ATATATATAATATAATTTTTGAAAACATATAAAATATAGAGTTTTTAAAATATTTTTGAAAAC
Found at i:599664 original size:9 final size:9
Alignment explanation
Indices: 599650--599695 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
599640 ATAAATACAG
599650 TATATATAT
1 TATATATAT
599659 TATATATAT
1 TATATATAT
599668 TAT-T-TAT
1 TATATATAT
599675 TATATAT-T
1 TATATATAT
599683 TAT-TATAT
1 TATATATAT
599691 TATAT
1 TATAT
599696 TGTTATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 9 0.27
8 10 0.30
9 14 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TATATATAT
Found at i:599666 original size:11 final size:10
Alignment explanation
Indices: 599650--599695 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
599640 ATAAATACAG
599650 TATATATATT
1 TATATATATT
599660 ATATATATTATT
1 -TATATA-TATT
599672 TATTATATATT
1 TA-TATATATT
599683 TAT-TATA-T
1 TATATATATT
599691 TATAT
1 TATAT
599696 TGTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 4 0.12
9 5 0.16
10 1 0.03
11 14 0.44
12 8 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATATATATT
Found at i:599677 original size:16 final size:16
Alignment explanation
Indices: 599654--599710 Score: 73
Period size: 16 Copynumber: 3.5 Consensus size: 16
599644 ATACAGTATA
599654 TATATTATATATATTAT
1 TATATTATATAT-TTAT
599671 T-TATTATATATTTAT
1 TATATTATATATTTAT
599686 TATATTATAT-TGTTAT
1 TATATTATATAT-TTAT
599702 TAATATTAT
1 T-ATATTAT
599711 TTTTCAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.16
16 23 0.62
17 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TATATTATATATTTAT
Found at i:599710 original size:9 final size:8
Alignment explanation
Indices: 599654--599711 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 8
599644 ATACAGTATA
599654 TATATTAT
1 TATATTAT
599662 ATATATTAT
1 -TATATTAT
599671 T-TATTA-
1 TATATTAT
599677 TATATTTAT
1 TATA-TTAT
599686 TATATTA-
1 TATATTAT
*
599693 TATTGTTAT
1 TA-TATTAT
599702 TAATATTAT
1 T-ATATTAT
599711 T
1 T
599712 TTTCAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
6 1 0.02
7 9 0.22
8 11 0.27
9 19 0.46
10 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:604657 original size:18 final size:19
Alignment explanation
Indices: 604634--604672 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
604624 TTTAAATAGT
604634 AATAAAAACGATTAAA-TA
1 AATAAAAACGATTAAAGTA
* *
604652 AATAAAAGCTATTAAAGTA
1 AATAAAAACGATTAAAGTA
604671 AA
1 AA
604673 AATAAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (19 bp):
AATAAAAACGATTAAAGTA
Found at i:608141 original size:6 final size:6
Alignment explanation
Indices: 608126--608165 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
608116 AGAAGAAAGA
608126 AAAAAT -AAAAT AAAAAT -AAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
608166 GTAACGGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:608142 original size:11 final size:11
Alignment explanation
Indices: 608126--608165 Score: 71
Period size: 11 Copynumber: 3.5 Consensus size: 11
608116 AGAAGAAAGA
608126 AAAAATAAAAT
1 AAAAATAAAAT
608137 AAAAATAAAAT
1 AAAAATAAAAT
608148 AAAAATAAAAAT
1 AAAAAT-AAAAT
608160 AAAAAT
1 AAAAAT
608166 GTAACGGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:618416 original size:2 final size:2
Alignment explanation
Indices: 618360--618408 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
618350 AATACGAAGA
*
618360 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
618401 AT AT AT AT
1 AT AT AT AT
618409 TGTATATAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:620920 original size:39 final size:39
Alignment explanation
Indices: 620866--620944 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
620856 AATAGCTTTC
620866 CTTGGTCGCTCATAAGAATCATAAATCTGGACAAATTGT
1 CTTGGTCGCTCATAAGAATCATAAATCTGGACAAATTGT
*
620905 CTTGGTCGCTCATAAGAATCATTAATCTGGACAAATTGT
1 CTTGGTCGCTCATAAGAATCATAAATCTGGACAAATTGT
620944 C
1 C
620945 CTATGTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (39 bp):
CTTGGTCGCTCATAAGAATCATAAATCTGGACAAATTGT
Found at i:623270 original size:32 final size:32
Alignment explanation
Indices: 623234--623294 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
623224 AAAGACAAAT
* *
623234 TTATAATTTGAATCTTAAATTTTTTTTTATGA
1 TTATAATTTGAATATTAAATTATTTTTTATGA
623266 TTATAATTTGAATATTAAATTATTTTTTA
1 TTATAATTTGAATATTAAATTATTTTTTA
623295 ATAATTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (32 bp):
TTATAATTTGAATATTAAATTATTTTTTATGA
Found at i:624170 original size:2 final size:2
Alignment explanation
Indices: 624163--624253 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
624153 AGAACAAAAC
624163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
624205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
624247 TA TA TA T
1 TA TA TA T
624254 CATCATACAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:624412 original size:23 final size:23
Alignment explanation
Indices: 624386--624441 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
624376 CACCGAAGTG
*
624386 CCACGTGGAAATGTCCCAAAAGA
1 CCACGTAGAAATGTCCCAAAAGA
* * * *
624409 CCACATAGATATGTCCCCAAGGA
1 CCACGTAGAAATGTCCCAAAAGA
624432 CCACGTAGAA
1 CCACGTAGAA
624442 TTATCCCGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.29, G:0.20, T:0.14
Consensus pattern (23 bp):
CCACGTAGAAATGTCCCAAAAGA
Found at i:624617 original size:45 final size:45
Alignment explanation
Indices: 624541--624729 Score: 200
Period size: 45 Copynumber: 4.2 Consensus size: 45
624531 TTATAACATT
* *** * * * *
624541 TCACATAGCTTGTATCACATAAACATATAATCACATTGATCATTG
1 TCACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAATG
*
624586 TCACATAACTTATATCACATTTTCATGTAATCACATAGGTCAATG
1 TCACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAATG
* * * *
624631 -CTACATAGTTTATATCTCATTTTCATTTAGTCACATAGGTCAATG
1 TC-ACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAATG
* * * *
624676 CCACATAGCTTATATCTCATTTTCATGTAATCATATAGGTCAATA
1 TCACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAATG
*
624721 TCATATAGC
1 TCACATAGC
624730 ATAAAATATA
Statistics
Matches: 121, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
44 1 0.01
45 119 0.98
46 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (45 bp):
TCACATAGCTTATATCACATTTTCATGTAATCACATAGGTCAATG
Found at i:631001 original size:16 final size:15
Alignment explanation
Indices: 630967--631031 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 15
630957 TTATAACATT
*
630967 TCACATA-ACTTATA
1 TCACATAGACATATA
630981 TCACATAGACATATAA
1 TCACATAGACATAT-A
*
630997 TCACATAGATCAT-TG
1 TCACATAGA-CATATA
* *
631012 TCATATA-ACTTATA
1 TCACATAGACATATA
631026 TCACAT
1 TCACAT
631032 TTTCATGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 2 0.05
14 14 0.34
15 11 0.27
16 11 0.27
17 3 0.07
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.34
Consensus pattern (15 bp):
TCACATAGACATATA
Found at i:631069 original size:45 final size:45
Alignment explanation
Indices: 630968--631143 Score: 217
Period size: 45 Copynumber: 3.9 Consensus size: 45
630958 TATAACATTT
*** * * *
630968 CACATAACTTATATCACATAGACATATAATCACATAGATCATTGT
1 CACATAACTTATATCACATTTTCATATAATCACATAGGTCAATGC
* *
631013 CATATAACTTATATCACATTTTCATGTAATCACATAGGTCAATGC
1 CACATAACTTATATCACATTTTCATATAATCACATAGGTCAATGC
* ** *
631058 CACATAGCTTATATTTCATTTTCATATAATCATATAGGTCAATGC
1 CACATAACTTATATCACATTTTCATATAATCACATAGGTCAATGC
* * *
631103 CACATACCTTATATCTCATTTTCATGTAATCACATAGGTCA
1 CACATAACTTATATCACATTTTCATATAATCACATAGGTCA
631144 GTATCATATA
Statistics
Matches: 113, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 113 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (45 bp):
CACATAACTTATATCACATTTTCATATAATCACATAGGTCAATGC
Found at i:643042 original size:58 final size:58
Alignment explanation
Indices: 642873--643383 Score: 824
Period size: 58 Copynumber: 8.8 Consensus size: 58
642863 ATGACACTAA
*
642873 GTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGAGCACTTC
1 GTGTGCAAAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* *
642932 GTGTGCAAAAATGTTAAGAAACTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
1 GTGTGCAAAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* *
642991 ATGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTTTTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* *
643049 GTTTGCAAAAATGTTAAGAAATTCATACTAAGTGTATTAATTTCCGTATTGGGCACTTC
1 GTGTGCAAAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
643108 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* * *
643166 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATATCCATATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
*
643224 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
* * * *
643282 ATGTGCAAAAAGTTAAAAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
** * *
643340 GTGTGCAAACCGTTAAGATATTCATATTAAGTGTATGAATTTCC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCC
643384 ATATGGGAAA
Statistics
Matches: 421, Mismatches: 30, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
58 300 0.71
59 121 0.29
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTC
Found at i:643642 original size:68 final size:68
Alignment explanation
Indices: 643531--643838 Score: 508
Period size: 68 Copynumber: 4.5 Consensus size: 68
643521 ATAGTATTTA
* * * *
643531 TTGACAGAAAGGTATCATTTATGCCAGTTAGATGAAAGTCTAAGTGCCTTTGAGGCCTAACTGTG
1 TTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGACTTTGAAGCCTAACTGTG
643596 CAT
66 CAT
*
643599 TTGACAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAGTGACTTTGAAGCCTAACTGTG
1 TTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGACTTTGAAGCCTAACTGTG
643664 CAT
66 CAT
* *
643667 TTGACAGAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAGTGACTTTGAAGCCTAATTGTG
1 TTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGACTTTGAAGCCTAACTGTG
643732 CAT
66 CAT
* * *
643735 TTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAAGCCTAACTATG
1 TTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGACTTTGAAGCCTAACTGTG
643800 CAT
66 CAT
* *
643803 TTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAA
1 TTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
643839 CGGTCAAATG
Statistics
Matches: 226, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 226 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (68 bp):
TTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGACTTTGAAGCCTAACTGTG
CAT
Found at i:645314 original size:59 final size:59
Alignment explanation
Indices: 645222--645340 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
645212 GTAGACCAGT
645222 CCTTCGGTATGAAGACTAGAGGTCTCGAGACCAAGCATCTGGTCTCGATACGGAGCATC
1 CCTTCGGTATGAAGACTAGAGGTCTCGAGACCAAGCATCTGGTCTCGATACGGAGCATC
*
645281 CCTTCGGTATGAAGACTAGAGGTCTCGAGACCAAGCATCTGGTTTCGATACGGAGCATC
1 CCTTCGGTATGAAGACTAGAGGTCTCGAGACCAAGCATCTGGTCTCGATACGGAGCATC
645340 C
1 C
645341 GATATCGATA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (59 bp):
CCTTCGGTATGAAGACTAGAGGTCTCGAGACCAAGCATCTGGTCTCGATACGGAGCATC
Found at i:647938 original size:25 final size:27
Alignment explanation
Indices: 647890--647943 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
647880 TATATGTACA
* *
647890 TATATATTTTTATTTAATCATTTTCTT
1 TATATATTTTAATTTAATCATTTTATT
*
647917 TATATGTTTTAATTT-ATC-TTTTATT
1 TATATATTTTAATTTAATCATTTTATT
647942 TA
1 TA
647944 AAATATCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 3 0.12
27 13 0.54
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.67
Consensus pattern (27 bp):
TATATATTTTAATTTAATCATTTTATT
Found at i:657552 original size:17 final size:17
Alignment explanation
Indices: 657530--657568 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
657520 TGAATCAAAT
657530 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
657547 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
657564 -AATTA
1 TAATTA
657569 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:659798 original size:22 final size:23
Alignment explanation
Indices: 659751--659798 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
659741 CACCGTAGTG
*
659751 CCACATAAGATTGTCCATAAGGA
1 CCACATAAGATTGTCCATAAGAA
*
659774 CCACATATA-ATT-TCCTTAAGAA
1 CCACATA-AGATTGTCCATAAGAA
659796 CCA
1 CCA
659799 TATACATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 10 0.45
24 1 0.05
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (23 bp):
CCACATAAGATTGTCCATAAGAA
Found at i:659976 original size:105 final size:105
Alignment explanation
Indices: 659785--659991 Score: 281
Period size: 105 Copynumber: 2.0 Consensus size: 105
659775 CACATATAAT
* * *
659785 TTCCTTAAGAACCATATACATATATCAAGGATCAAGTAAGTGTCTCAAAAGACCTCATACATGCT
1 TTCCTTAAGAACCATATACATATATCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACATGCT
659850 CCAAAGAATACATATACGTCCCGAAGGACCCCGTAGAAAA
66 CCAAAGAATACATATACGTCCCGAAGGACCCCGTAGAAAA
* * * * *
659890 TTCCTTAAGAATCATATACATAT-GCTAAGGACCAAATACGTGTCGCAAAAGACCTCATAGATGT
1 TTCCTTAAGAACCATATACATATATC-AAGGACCAAATAAGTGTCGCAAAAGACCTCATACATGC
* * * * *
659954 TCCATAGGATACCTATATGTCCCGAAGGACCGCGTAGA
65 TCCAAAGAATACATATACGTCCCGAAGGACCCCGTAGA
659992 CCCTCGACTC
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 1 0.01
105 87 0.99
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (105 bp):
TTCCTTAAGAACCATATACATATATCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACATGCT
CCAAAGAATACATATACGTCCCGAAGGACCCCGTAGAAAA
Found at i:663522 original size:22 final size:22
Alignment explanation
Indices: 663497--663538 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
663487 CATAAATTTC
663497 TTCAATCCTTCATTTAAATAAT
1 TTCAATCCTTCATTTAAATAAT
663519 TTCAATCCTTCATTTAAATA
1 TTCAATCCTTCATTTAAATA
663539 TTAAGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (22 bp):
TTCAATCCTTCATTTAAATAAT
Found at i:663574 original size:23 final size:24
Alignment explanation
Indices: 663530--663575 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
663520 TCAATCCTTC
663530 ATTTAAATATTAAGTTTTTTAAAT
1 ATTTAAATATTAAGTTTTTTAAAT
*
663554 ATTTAAATA-TAATTTTTTTAAA
1 ATTTAAATATTAAGTTTTTTAAA
663576 CATACACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTAAATATTAAGTTTTTTAAAT
Found at i:672927 original size:21 final size:21
Alignment explanation
Indices: 672896--672954 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
672886 GTCCGAGTTA
*
672896 CCCGTGACGGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
*
672917 TCCGCGACGGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
*
672938 CCCTCGACGGCCGCAAT
1 CCCGCGACGGCCGCAAT
672955 CACGGTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.19, C:0.41, G:0.31, T:0.10
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAGCG
Found at i:675410 original size:32 final size:32
Alignment explanation
Indices: 675338--675413 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
675328 AACTGGTATT
* *
675338 ACCCAACTTGTTTTCAACCTGACCTGTGATGA
1 ACCCGACTTGTTTTCAACCTGACCTGTAATGA
** * *
675370 ACTTGACTTGTTTTTAACTTGACCTGTAAATG-
1 ACCCGACTTGTTTTCAACCTGACCTGT-AATGA
675402 ACCCGACTTGTT
1 ACCCGACTTGTT
675414 ATTGACTGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 32 0.91
33 3 0.09
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (32 bp):
ACCCGACTTGTTTTCAACCTGACCTGTAATGA
Found at i:675722 original size:23 final size:24
Alignment explanation
Indices: 675681--675734 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
675671 CAATGATTAA
675681 ATGTAAATTAGTATAGTTTAATTT
1 ATGTAAATTAGTATAGTTTAATTT
675705 ATGTAAATTA-TATAGTTTAATTT
1 ATGTAAATTAGTATAGTTTAATTT
675728 ATGTAAA
1 ATGTAAA
675735 AAAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAGTATAGTTTAATTT
Found at i:675847 original size:22 final size:23
Alignment explanation
Indices: 675810--675852 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
675800 TACAAATAAT
*
675810 TTTGACAATGAAATGATTATTAA
1 TTTGACAATGAAATGAGTATTAA
*
675833 TTTGATAAT-AAATGAGTATT
1 TTTGACAATGAAATGAGTATT
675853 GGTATTGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (23 bp):
TTTGACAATGAAATGAGTATTAA
Found at i:676011 original size:12 final size:11
Alignment explanation
Indices: 675985--676024 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
675975 GATAATGATA
*
675985 ATTTAAATAAC
1 ATTTGAATAAC
*
675996 ATTTGATATAAA
1 ATTTGA-ATAAC
676008 ATTTGAATAAC
1 ATTTGAATAAC
676019 ATTTGA
1 ATTTGA
676025 GTTAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTGAATAAC
Found at i:682236 original size:23 final size:23
Alignment explanation
Indices: 682186--682266 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
682176 GCAGAACCCT
682186 AGGGGGATATCGATTCCCC-T---
1 AGGGGGA-ATCGATTCCCCTTCAA
*
682206 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTCAA
682229 AGGGGGAATCGATTCCCCTTC-A
1 AGGGGGAATCGATTCCCCTTCAA
682251 A--GGGATATCGATTCCC
1 AGGGGGA-ATCGATTCCC
682267 TCTGCCCTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.19
20 12 0.22
21 10 0.19
22 2 0.04
23 20 0.37
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGATTCCCCTTCAA
Found at i:687814 original size:6 final size:6
Alignment explanation
Indices: 687783--687893 Score: 89
Period size: 6 Copynumber: 19.7 Consensus size: 6
687773 TATATAATTT
* * *
687783 ATATTA ATA-AA ATATTT ATAATTA ATATTA ATA-TA A-ATTA TTTATT-
1 ATATTA ATATTA ATATTA AT-ATTA ATATTA ATATTA ATATTA -ATATTA
687829 ATAATTA ATATTA ATATTA ATA-T- A-ATTA ATATTA ATATTA ATATTA
1 AT-ATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
*
687875 A-CTT- ATATTA ATA-TA ATAT
1 ATATTA ATATTA ATATTA ATAT
687894 AGTTTATAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
3 1 0.01
4 4 0.05
5 21 0.25
6 48 0.57
7 10 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:687913 original size:50 final size:47
Alignment explanation
Indices: 687781--687922 Score: 155
Period size: 50 Copynumber: 2.9 Consensus size: 47
687771 CCTATATAAT
* *
687781 TTATATTAATA-AA-ATATTTATAATTAATATTAATATAAATTATTTA
1 TTATATTAATATAATATATTTATAATTAATATTAATATTAA-TATTAA
*
687827 TTATAATTAATATTAATAT-TAATATAATTAATATTAATATTAATATTAA
1 TTAT-ATTAATA-TAATATAT-TTATAATTAATATTAATATTAATATTAA
**
687876 CTTATATTAATATAATATAGTTTATAATTTGTAATTAATATTAATAT
1 -TTATATTAATATAATATA-TTTATAATTAAT-ATTAATATTAATAT
687923 AAAATATAGT
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
46 4 0.05
47 7 0.09
48 6 0.07
49 23 0.28
50 41 0.51
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (47 bp):
TTATATTAATATAATATATTTATAATTAATATTAATATTAATATTAA
Found at i:688774 original size:20 final size:20
Alignment explanation
Indices: 688749--688803 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
688739 CAATTTTGAA
*
688749 GGTGCATCGATTCATTAAGG
1 GGTGCATCGATGCATTAAGG
688769 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
*
688789 GATGCATCGATGCAT
1 GGTGCATCGATGCAT
688804 GGAAATGTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.27
Consensus pattern (20 bp):
GGTGCATCGATGCATTAAGG
Found at i:689647 original size:32 final size:31
Alignment explanation
Indices: 689606--689698 Score: 98
Period size: 32 Copynumber: 3.0 Consensus size: 31
689596 AGTCGAGGGT
*
689606 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTTCGGAACATATGGACAG-A
* * *
689638 TTACCTATG-TCTTTCGGGACATATGGACTGT
1 TTACCTATGTTC-TTCGGAACATATGGACAGA
* * *
689669 TTACCTAGGTTCTTCGGTACCTATGGACAG
1 TTACCTATGTTCTTCGGAACATATGGACAG
689699 TTGCCGAGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
31 25 0.49
32 26 0.51
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACAGA
Found at i:689685 original size:31 final size:31
Alignment explanation
Indices: 689604--689700 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
689594 AGAGTCGAGG
*
689604 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTTCGGAACATATGGACA
* * *
689635 GAATTACCTATG-TCTTTCGGGACATATGGACT
1 G-TTTACCTATGTTC-TTCGGAACATATGGACA
* * *
689667 GTTTACCTAGGTTCTTCGGTACCTATGGACA
1 GTTTACCTATGTTCTTCGGAACATATGGACA
689698 GTT
1 GTT
689701 GCCGAGGTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
31 28 0.52
32 26 0.48
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACA
Found at i:690523 original size:22 final size:22
Alignment explanation
Indices: 690484--690526 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
690474 GCACTGTAGC
* * *
690484 ACTGTTCATGGTATTGTTCATT
1 ACTGTTCACGATAATGTTCATT
690506 ACTGTTCACGATAATGTTCAT
1 ACTGTTCACGATAATGTTCAT
690527 ATAGTATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.44
Consensus pattern (22 bp):
ACTGTTCACGATAATGTTCATT
Found at i:690796 original size:13 final size:13
Alignment explanation
Indices: 690764--690790 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
690754 ACTATATACT
690764 ATATATAAATATA
1 ATATATAAATATA
690777 ATATATAAATATA
1 ATATATAAATATA
690790 A
1 A
690791 ATTATAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATATAAATATA
Found at i:690796 original size:15 final size:15
Alignment explanation
Indices: 690765--690841 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
690755 CTATATACTA
690765 TATATAAATAT-AA-
1 TATATAAATATAAAT
690778 TATATAAATATAAAT
1 TATATAAATATAAAT
* *
690793 TATAGTTAAGAT-AAT
1 TATA-TAAATATAAAT
* *
690808 TAGTATTAATATAAAC
1 TA-TATAAATATAAAT
**
690824 TATA-ATTTATAAAT
1 TATATAAATATAAAT
690838 TATA
1 TATA
690842 AACTATAGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 11 0.22
14 12 0.24
15 17 0.33
16 11 0.22
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (15 bp):
TATATAAATATAAAT
Found at i:690843 original size:21 final size:21
Alignment explanation
Indices: 690817--690890 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
690807 TTAGTATTAA
*
690817 TATAAACTATAATTTATAAAT
1 TATAAACTATAGTTTATAAAT
690838 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGTTTATAAAT
* * *
690859 TATATACTATAGGTTATAAAG
1 TATAAACTATAGTTTATAAAT
690880 TATAAACTATA
1 TATAAACTATA
690891 TAGTACACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
TATAAACTATAGTTTATAAAT
Found at i:690960 original size:20 final size:21
Alignment explanation
Indices: 690930--691036 Score: 86
Period size: 20 Copynumber: 5.2 Consensus size: 21
690920 AAGTATAGGT
690930 TACATAT--ATAGTTTATATA
1 TACATATAAATAGTTTATATA
690949 -ACATATAAATAGATTGTATATA
1 TACATATAAATAG-TT-TATATA
*
690971 TACATATATACTATAGGTTATATA
1 TACATATA-A--ATAGTTTATATA
690995 T--ATAT--ATAGTTTATATA
1 TACATATAAATAGTTTATATA
* *
691012 TAC-TATACATAGTTTATACA
1 TACATATAAATAGTTTATATA
691032 TACAT
1 TACAT
691037 GTACTATAAG
Statistics
Matches: 72, Mismatches: 3, Indels: 24
0.73 0.03 0.24
Matches are distributed among these distances:
17 12 0.17
18 9 0.12
20 18 0.25
21 3 0.04
22 10 0.14
23 7 0.10
24 8 0.11
25 1 0.01
26 4 0.06
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (21 bp):
TACATATAAATAGTTTATATA
Found at i:691002 original size:17 final size:17
Alignment explanation
Indices: 690974--691018 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
690964 GTATATATAC
690974 ATATATACTATAGGTTAT
1 ATATATA-TATAGGTTAT
*
690992 ATATATATATAGTTTAT
1 ATATATATATAGGTTAT
691009 ATATACTATA
1 ATATA-TATA
691019 CATAGTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (17 bp):
ATATATATATAGGTTAT
Found at i:691523 original size:90 final size:88
Alignment explanation
Indices: 691371--691540 Score: 295
Period size: 90 Copynumber: 1.9 Consensus size: 88
691361 ACACACCCTT
691371 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
691436 ATTAATTAGAATTTAATAATCCTC
66 ATTAATT-GAAATTAATAATCCTC
* *
691460 TTATATCCAAGTTACCCTAATTATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
691525 AATTAATTGAAATTAA
65 AATTAATTGAAATTAA
691541 ATATTTGGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 36 0.47
90 41 0.53
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:692765 original size:7 final size:7
Alignment explanation
Indices: 692746--692777 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
692736 ATAATTTAAG
692746 GTTTAGA
1 GTTTAGA
*
692753 GTTTAGG
1 GTTTAGA
692760 GTTTAGA
1 GTTTAGA
692767 GTTTAGA
1 GTTTAGA
692774 GTTT
1 GTTT
692778 CTATAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (7 bp):
GTTTAGA
Found at i:692772 original size:14 final size:14
Alignment explanation
Indices: 692710--692777 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
692700 TAGTTTATAA
692710 AGTTTAGGGTTTA-
1 AGTTTAGGGTTTAG
* * *
692723 AGATCTAAGGTTTAT
1 AG-TTTAGGGTTTAG
* *
692738 AATTTAAGGTTTAG
1 AGTTTAGGGTTTAG
692752 AGTTTAGGGTTTAG
1 AGTTTAGGGTTTAG
*
692766 AGTTTAGAGTTT
1 AGTTTAGGGTTT
692778 CTATAAACTA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
13 2 0.04
14 42 0.93
15 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.44
Consensus pattern (14 bp):
AGTTTAGGGTTTAG
Found at i:692838 original size:2 final size:2
Alignment explanation
Indices: 692827--693031 Score: 138
Period size: 2 Copynumber: 107.5 Consensus size: 2
692817 ATAGTATTTC
*
692827 TA TA -A TA TA TA TA TA T- TA CT- TA TA T- TA GT- TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA
* *
692866 TA TA TA TA TA TA TA CTA TA T- TA -A TA TA -A TT TA TA -A TT TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
692905 TA AA CTA TA TA T- TT TA TA TA T- TT TA TA TA TA TA TA TA -A TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
692945 TA T- TA -A TA TA AA TA TA GTT TA TA TA TA TA GTT TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
692987 CT- TA TA T- TA TA TA TA TA TA TA TA TA TA TA 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
693027 TA TA T
1 TA TA T
693032 TTTTTTCAAT
Statistics
Matches: 161, Mismatches: 18, Indels: 48
0.71 0.08 0.21
Matches are distributed among these distances:
1 17 0.11
2 137 0.85
3 7 0.04
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:692922 original size:9 final size:9
Alignment explanation
Indices: 692910--692934 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
692900 ATTTATAAAC
692910 TATATATTT
1 TATATATTT
692919 TATATATTT
1 TATATATTT
692928 TATATAT
1 TATATAT
692935 ATATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TATATATTT
Found at i:693674 original size:16 final size:15
Alignment explanation
Indices: 693653--693686 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
693643 TAGTATTTAT
693653 CTGTTTCAGACATGAA
1 CTGTTT-AGACATGAA
*
693669 CTGTTTTGACATGAA
1 CTGTTTAGACATGAA
693684 CTG
1 CTG
693687 ACATCGATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (15 bp):
CTGTTTAGACATGAA
Found at i:705296 original size:14 final size:14
Alignment explanation
Indices: 705277--705318 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
705267 TTTAGATTTT
705277 TTAAAAT-TACATTA
1 TTAAAATATA-ATTA
705291 TTAAAAATATAATTA
1 TT-AAAATATAATTA
705306 TTAAAAATATAAT
1 TT-AAAATATAAT
705319 AAAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAAATATAATTA
Found at i:705320 original size:18 final size:15
Alignment explanation
Indices: 705287--705318 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
705277 TTAAAATTAC
705287 ATTATTAAAAATATA
1 ATTATTAAAAATATA
705302 ATTATTAAAAATATA
1 ATTATTAAAAATATA
705317 AT
1 AT
705319 AAAAATATAT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTATTAAAAATATA
Found at i:705429 original size:17 final size:17
Alignment explanation
Indices: 705407--705440 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
705397 CAAGTTTGAA
705407 TTCGAATTTGAATCGAG
1 TTCGAATTTGAATCGAG
705424 TTCGAATTTGAATCGAG
1 TTCGAATTTGAATCGAG
705441 CTCAAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (17 bp):
TTCGAATTTGAATCGAG
Found at i:709893 original size:34 final size:33
Alignment explanation
Indices: 709802--709900 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
709792 ATTTTGCAAG
* *
709802 TTGGAAAATTCATCTTGGTTGGTAGACAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
709835 TTGG-AAATATCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAAT-TCATCTTGGTTGGTGGCCAACTTA
* *
709868 TTGGAAAATTTATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
709901 TGCACATGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
32 4 0.07
33 34 0.58
34 21 0.36
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:714751 original size:32 final size:33
Alignment explanation
Indices: 714672--714802 Score: 219
Period size: 33 Copynumber: 4.0 Consensus size: 33
714662 ATTTGGCAAG
714672 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
714705 TTGGAAAATTCATCTTAGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
714738 TTGG-AAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
714770 TTGGAAAATTTATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
714803 TGCACATGAG
Statistics
Matches: 92, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
32 31 0.34
33 44 0.48
34 17 0.18
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:714751 original size:65 final size:67
Alignment explanation
Indices: 714672--714802 Score: 221
Period size: 65 Copynumber: 2.0 Consensus size: 67
714662 ATTTGGCAAG
*
714672 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTATTGGAAAATTCATC-TTAGTTGGTGGCCAACT
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTATTGGAAAATTCATCTTTAGTAGGTGGCCAACT
714736 TA
66 TA
* *
714738 TTGG-AAATTCATCTTGGTTGGTGGCCAACTTATTGGAAAATTTATCTTTGGTAGGTGGCCAACT
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTATTGGAAAATTCATCTTTAGTAGGTGGCCAACT
714802 T
66 T
714803 TGCACATGAG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 41 0.67
66 20 0.33
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (67 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTATTGGAAAATTCATCTTTAGTAGGTGGCCAACT
TA
Found at i:718316 original size:20 final size:20
Alignment explanation
Indices: 718291--718329 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
718281 TATGGTGTCG
*
718291 TATATATTCGTTTTATATAT
1 TATATATTCATTTTATATAT
718311 TATATATTCATTTTATATA
1 TATATATTCATTTTATATA
718330 GTATGTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (20 bp):
TATATATTCATTTTATATAT
Found at i:719226 original size:2 final size:2
Alignment explanation
Indices: 719219--719269 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
719209 TCTATGTTTC
719219 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
719261 TA TA TA TA T
1 TA TA TA TA T
719270 TAGTTTACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:719358 original size:41 final size:40
Alignment explanation
Indices: 719285--719387 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 40
719275 TACAAATGGT
**
719285 TTTTGAAAATACGTAT-ATA-ATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATAATATATATATAGTTTTTAAAACA
719323 TTTTAGAAAATATATATAATATATATATAGTTTTTAAAATCA
1 TTTT-GAAAATATATATAATATATATATAGTTTTTAAAA-CA
719365 TTTTGAAAA-ATATATAATATATA
1 TTTTGAAAATATATATAATATATA
719388 GTTCTTTTGA
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
38 4 0.07
39 10 0.17
40 17 0.29
41 22 0.37
42 6 0.10
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (40 bp):
TTTTGAAAATATATATAATATATATATAGTTTTTAAAACA
Found at i:719406 original size:26 final size:27
Alignment explanation
Indices: 719365--719416 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
719355 TTTAAAATCA
*
719365 TTTTGAAAAATATATAATATATAGTTC
1 TTTTGAAAAACATATAATATATAGTTC
*
719392 TTTTG-AAAACATATATTATATAGTT
1 TTTTGAAAAACATATAATATATAGTT
719417 TTGAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (27 bp):
TTTTGAAAAACATATAATATATAGTTC
Found at i:719412 original size:103 final size:102
Alignment explanation
Indices: 719298--719553 Score: 276
Period size: 102 Copynumber: 2.5 Consensus size: 102
719288 TGAAAATACG
*
719298 TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATATATAGTTTTT-AAAA
1 TATATATTATATAGTTTTTAAAACATTTT-GAAAATATATATAATATATATATAGTTTTTGAAAA
*
719362 TCA-TTTTGAAAA-ATATATAATATATAGTTCTTTTGAAAAC
65 -CATTTTTGAAAACATATATAATACATAG---TTTTGAAAAC
* * **
719402 -ATATATTATATAGTTTTGAAAATATTTTTTAAA-ATATAT-ATA-ATATATAGTTTTTGAAAAC
1 TATATATTATATAGTTTTTAAAACATTTTGAAAATATATATAATATATATATAGTTTTTGAAAAC
* *
719463 ATTTTTGAAAACTTATATATTACATAGTTTTGAAAAC
66 ATTTTTGAAAACATATATAATACATAGTTTTGAAAAC
*
719500 ATTTATATATTATATAGTTTTT-AAACGTTTTTGAAAACTTATATATAATATATA
1 ---TATATATTATATAGTTTTTAAAAC-ATTTTGAAAA--TATATATAATATATA
719554 GTTTATATTA
Statistics
Matches: 126, Mismatches: 13, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
98 10 0.08
99 15 0.12
100 16 0.13
101 21 0.17
102 27 0.21
103 25 0.20
105 6 0.05
106 3 0.02
107 3 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (102 bp):
TATATATTATATAGTTTTTAAAACATTTTGAAAATATATATAATATATATATAGTTTTTGAAAAC
ATTTTTGAAAACATATATAATACATAGTTTTGAAAAC
Found at i:719436 original size:61 final size:61
Alignment explanation
Indices: 719341--719464 Score: 173
Period size: 61 Copynumber: 2.0 Consensus size: 61
719331 AATATATATA
*
719341 ATATATATATAGTTTTTAAAATCATTTTG-AAAA-ATATATAATATATAGTTCTTTTGAAAAC
1 ATATATATATAGTTTTGAAAATCATTTTGAAAAATATATATAATATATAG-T-TTTTGAAAAC
**
719402 ATATATTATATAGTTTTGAAAAT-ATTTTTTAAAATATATATAATATATAGTTTTTGAAAAC
1 ATATA-TATATAGTTTTGAAAATCATTTTGAAAAATATATATAATATATAGTTTTTGAAAAC
719463 AT
1 AT
719465 TTTTGAAAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
61 22 0.38
62 21 0.36
63 15 0.26
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (61 bp):
ATATATATATAGTTTTGAAAATCATTTTGAAAAATATATATAATATATAGTTTTTGAAAAC
Found at i:719467 original size:38 final size:37
Alignment explanation
Indices: 719392--719503 Score: 149
Period size: 38 Copynumber: 3.1 Consensus size: 37
719382 TATATAGTTC
*
719392 TTTTGAAAAC--ATATATTATATAGTTTTGAAAATAT
1 TTTTGAAAACTTATATATTATATAGTTTTGAAAACAT
* *
719427 TTTTTAAAA-TATATATAATATATAGTTTTTGAAAACAT
1 TTTTGAAAACT-TATATATTATATAG-TTTTGAAAACAT
*
719465 TTTTGAAAACTTATATATTACATAGTTTTGAAAACAT
1 TTTTGAAAACTTATATATTATATAGTTTTGAAAACAT
719502 TT
1 TT
719504 ATATATTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
35 8 0.12
37 26 0.39
38 31 0.47
39 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTGAAAACTTATATATTATATAGTTTTGAAAACAT
Found at i:719493 original size:25 final size:26
Alignment explanation
Indices: 719465--719520 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
719455 TTGAAAACAT
719465 TTTTGAAAAC-TTATATATTACATAG
1 TTTTGAAAACATTATATATTACATAG
*
719490 TTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAACA-TTATATATTACATAG
719517 TTTT
1 TTTT
719521 TAAACGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 10 0.36
27 18 0.64
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (26 bp):
TTTTGAAAACATTATATATTACATAG
Found at i:722012 original size:2 final size:2
Alignment explanation
Indices: 722005--722053 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
721995 AAATAACGTT
722005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
722047 TA TA TA T
1 TA TA TA T
722054 GTTAGTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:722108 original size:13 final size:13
Alignment explanation
Indices: 722090--722119 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
722080 TTAACTAAAC
722090 TTTTATTCAAATA
1 TTTTATTCAAATA
*
722103 TTTTATTCGAATA
1 TTTTATTCAAATA
722116 TTTT
1 TTTT
722120 TCAAGAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (13 bp):
TTTTATTCAAATA
Found at i:722811 original size:26 final size:24
Alignment explanation
Indices: 722782--722832 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
722772 ATCCCCAAAA
*
722782 TTTTCAAATAAAAGTCATAATTGTTT
1 TTTTAAAATAAAAGT--TAATTGTTT
*
722808 TTTTAAAATAATAGTTAATTGTTT
1 TTTTAAAATAAAAGTTAATTGTTT
722832 T
1 T
722833 ATAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
26 13 0.57
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTTAAAATAAAAGTTAATTGTTT
Found at i:722839 original size:24 final size:24
Alignment explanation
Indices: 722799--722848 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
722789 ATAAAAGTCA
* * *
722799 TAATTGTTTTTTTAAAATAATAGT
1 TAATTGTTTTATAAAAAAAATAGT
*
722823 TAATTGTTTTATAAAAAAAATCGT
1 TAATTGTTTTATAAAAAAAATAGT
722847 TA
1 TA
722849 GGAATGTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (24 bp):
TAATTGTTTTATAAAAAAAATAGT
Found at i:733094 original size:6 final size:6
Alignment explanation
Indices: 733083--733117 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
733073 CACGCCACAC
* *
733083 GCATAT GCATAT GCATAT GCACAT GCACAT GCATA
1 GCATAT GCATAT GCATAT GCATAT GCATAT GCATA
733118 CGCGCGCGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (6 bp):
GCATAT
Found at i:736652 original size:62 final size:63
Alignment explanation
Indices: 736555--736680 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 63
736545 GTACCAATTA
736555 ATTTATCGGTTGTCTTTAATTGCGAAAATTGGAAATTTAAATTAAAACTTAAAAACCC-ATTC
1 ATTTATCGGTTGTCTTTAATTGCGAAAATTGGAAATTTAAATTAAAACTTAAAAACCCGATTC
736617 ATTTATCGGTTGTCTTTAATTGCGAAAATTGGAAATTTAAATTAAAACTTAAAAACCCGATTC
1 ATTTATCGGTTGTCTTTAATTGCGAAAATTGGAAATTTAAATTAAAACTTAAAAACCCGATTC
736680 A
1 A
736681 AATTACTTAC
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 58 0.92
63 5 0.08
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.37
Consensus pattern (63 bp):
ATTTATCGGTTGTCTTTAATTGCGAAAATTGGAAATTTAAATTAAAACTTAAAAACCCGATTC
Found at i:736847 original size:15 final size:15
Alignment explanation
Indices: 736829--736879 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
736819 GTTGGAAAAA
736829 AATAAATAAAAAATG
1 AATAAATAAAAAATG
*
736844 AATAAGTAAAAAAATG
1 AATAAAT-AAAAAATG
736860 -ATAAAT-AAAAATAG
1 AATAAATAAAAAAT-G
736874 AATAAA
1 AATAAA
736880 ATATGATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 6 0.19
14 1 0.03
15 16 0.52
16 8 0.26
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.20
Consensus pattern (15 bp):
AATAAATAAAAAATG
Found at i:736848 original size:30 final size:32
Alignment explanation
Indices: 736791--736850 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
736781 TCAAAATAAA
736791 GAAAAATAAAAATTAAAAAATTAAATAAGTTG
1 GAAAAATAAAAATTAAAAAATTAAATAAGTTG
*
736823 GAAAAA-AATAAA-TAAAAAA-TGAATAAGT
1 GAAAAATAA-AAATTAAAAAATTAAATAAGT
736851 AAAAAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 8 0.31
31 9 0.35
32 9 0.35
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (32 bp):
GAAAAATAAAAATTAAAAAATTAAATAAGTTG
Found at i:736895 original size:25 final size:24
Alignment explanation
Indices: 736852--736899 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
736842 TGAATAAGTA
736852 AAAAAATGATAAATAAAAATAGAAT
1 AAAAAATGATAAATAAAAA-AGAAT
* * *
736877 AAAATATGATAATTTAAAAAGAA
1 AAAAAATGATAAATAAAAAAGAA
736900 AATAGTAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (24 bp):
AAAAAATGATAAATAAAAAAGAAT
Found at i:738030 original size:3 final size:3
Alignment explanation
Indices: 738024--738093 Score: 70
Period size: 3 Copynumber: 21.7 Consensus size: 3
738014 TATAGAAATA
*
738024 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT GAA- AAT AAA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT AAT
738070 AAT AAAT AAAT AAAT AAAT AAT AA
1 AAT -AAT -AAT -AAT -AAT AAT AA
738094 AAAAGTTTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.03
3 39 0.64
4 20 0.33
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:738044 original size:19 final size:19
Alignment explanation
Indices: 738020--738093 Score: 96
Period size: 19 Copynumber: 3.8 Consensus size: 19
738010 AAAATATAGA
738020 AATAAATAATAATAATAAT
1 AATAAATAATAATAATAAT
738039 AATAAATAATAATAATAAT
1 AATAAATAATAATAATAAT
* *
738058 AATGAA-AATAAAAATAAAT
1 AATAAATAATAATAAT-AAT
738077 AAATAAATAAATAATAA
1 -AATAAAT-AATAATAA
738094 AAAAGTTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 8 0.17
19 27 0.57
20 5 0.11
22 7 0.15
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (19 bp):
AATAAATAATAATAATAAT
Found at i:738094 original size:19 final size:16
Alignment explanation
Indices: 738027--738094 Score: 77
Period size: 16 Copynumber: 4.1 Consensus size: 16
738017 AGAAATAAAT
738027 AATAATAATAATAATA
1 AATAATAATAATAATA
738043 AATAATAATAATAAT-
1 AATAATAATAATAATA
*
738058 AATGAA-AATAAAAATA
1 AAT-AATAATAATAATA
738074 AATAAATAAATAAATAATA
1 AAT-AAT-AAT-AATAATA
738093 AA
1 AA
738095 AAAGTTTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 11 0.25
16 22 0.50
18 3 0.07
19 8 0.18
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:738207 original size:19 final size:20
Alignment explanation
Indices: 738180--738219 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
738170 TTAAAAACTA
*
738180 TATATGTTTTCAAAATATTT
1 TATATGTTTTCAAAACATTT
*
738200 TATA-GTTTTTAAAACATTT
1 TATATGTTTTCAAAACATTT
738219 T
1 T
738220 CAAAAACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TATATGTTTTCAAAACATTT
Found at i:738331 original size:33 final size:34
Alignment explanation
Indices: 738291--738368 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 34
738281 TTTGAAAAAC
*
738291 TATATATATGTTTTTAAAAAAATTTC-AAACTATA
1 TATATATATATTTTT-AAAAAATTTCAAAACTATA
* **
738325 TA-ATATATATTTTTGAAAGTTTTCAAAACTATA
1 TATATATATATTTTTAAAAAATTTCAAAACTATA
738358 TATATATATAT
1 TATATATATAT
738369 ATATATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 7 0.18
33 21 0.55
34 10 0.26
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (34 bp):
TATATATATATTTTTAAAAAATTTCAAAACTATA
Found at i:738361 original size:2 final size:2
Alignment explanation
Indices: 738354--738385 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
738344 TTTTCAAAAC
738354 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
738386 TAGAAAACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:738363 original size:32 final size:32
Alignment explanation
Indices: 738286--738366 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
738276 ATTTTTTTGA
*
738286 AAAACTATATATATGT-TTTTAAAAAAATTTC
1 AAAACTATATATATATATTTTAAAAAAATTTC
** **
738317 -AAACTATATAATATATATTTTTGAAAGTTTTC
1 AAAACTATAT-ATATATATTTTAAAAAAATTTC
738349 AAAACTATATATATATAT
1 AAAACTATATATATATAT
738367 ATATATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 9 0.21
31 5 0.12
32 19 0.45
33 9 0.21
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (32 bp):
AAAACTATATATATATATTTTAAAAAAATTTC
Found at i:739227 original size:84 final size:83
Alignment explanation
Indices: 739115--739661 Score: 625
Period size: 84 Copynumber: 6.5 Consensus size: 83
739105 ACCCTTATCT
* * * * * * *
739115 CCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAATCAAACTCGAAGGTCTTTTAT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
**
739180 TTTCAGATGACCCTTTTAG
66 TGGCAGAT-ACCCTTTTAG
* ** * * * * *
739199 CCCTGAGCTATACTACAAATGTTATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
*
739264 TGGCAAATAGCCCTTCTT-G
66 TGGCAGATA-CCCTT-TTAG
* * * *
739283 CCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTAAGCGTAGTAGAACTCGAAGGCCTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
*
739348 TGGCAGATAACCCTTCTAG
66 TGGCAGAT-ACCCTTTTAG
* * *
739367 CCTTGAGTTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * *
739432 TGGAAAATAACCCTTCTT-T
66 TGGCAGAT-ACCCTT-TTAG
* *
739451 CCTTGAGATATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
*
739516 TGGCAGATAACCTTTCTAG
66 TGGCAGATACCCTTT-TAG
* * *
739535 CCTTGAGTTATATTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
739600 TGGC-GAATAGCCCTTCTT-G
66 TGGCAG-ATA-CCCTT-TTAG
* * * *
739619 CCCTGAGTTATGTTGCAAATAATGTGCCTTGAAGCTGAGCGTA
1 CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTA
739662 TCTTTTATTG
Statistics
Matches: 398, Mismatches: 55, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
82 1 0.00
83 9 0.02
84 378 0.95
85 9 0.02
86 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (83 bp):
CCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
TGGCAGATACCCTTTTAG
Found at i:739314 original size:168 final size:167
Alignment explanation
Indices: 739115--739907 Score: 812
Period size: 168 Copynumber: 4.9 Consensus size: 167
739105 ACCCTTATCT
* * *
739115 CCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAATCAAACTCGAAGGTCTTTTAT
1 CCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTAT
** * * * * *
739180 TTTCAGATGACCCTTTTAGCCCTGAGCTATACTACAAATGTTATGCCTTTGAGCTGAGCGTAGTC
66 TGGCAGAT-ACCCTTTTAGCCTTGAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
*
739245 GAACTCGAAGGTTTTTTGTTGGCAAATAGCCCTTCTTG
130 GAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTG
* * * *
739283 CCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTAAGCGTAGT-AGAACTCGAAGGCCTTTTG
1 CCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCA-AACTCGAAGGTCTTTTA
* * * *
739347 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGT
65 TTGGCAGAT-ACCCTTTTAGCCTTGAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * *
739412 CGAACTCGAAGGTCTTTTGTTGGAAAATAACCCTTCTTT
129 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTG
* * *
739451 CCTTGAGATATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAT
1 CCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTAT
* *
739516 TGGCAGATAACCTTTCTAGCCTTGAGTTATATTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
66 TGGCAGATACCCTTT-TAGCCTTGAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
*
739581 GAACTCGAAGGTCTTTTGTTGGCGAATAGCCCTTCTTG
130 GAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTG
* *
739619 CCCTGAGTTATGTTGCAAATAATGTGCC-TTGAAGCTGAGC---G------T---A--TCTTTTA
1 CCTTGAGTTATGTTGCAAATGATGTGCCTTTG-AGCTGAGCGTAGTCAAACTCGAAGGTCTTTTA
* * * * * * * * *
739669 TTGGCAGATAACCCTTCTATCCTTGAGTTATGCTGGAAATGATGTTCCTTTGAGCTGAGTGTAAT
65 TTGGCAGAT-ACCCTTTTAGCCTTGAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* *
739734 CGAACTCCAAGGTC---T-TTGGCAAATAGGCCTTCTTG
129 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTG
* * * * * * *
739769 CCTTAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGTGTAATCGAATTCGAAGGTC---T-T
1 CCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTAT
* * * * * * *
739829 TGGCAGATAGCCCTTCTT-GCCTTAAGCTATGCTGAAAATGATTTGCCTT-GAGCTGAGTGTAAT
66 TGGCAGATA-CCCTT-TTAGCCTTGAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* *
739892 CGAAGTTGAAGGTCTT
129 CGAACTCGAAGGTCTT
739908 CGGTAGATAA
Statistics
Matches: 528, Mismatches: 74, Indels: 54
0.80 0.11 0.08
Matches are distributed among these distances:
149 7 0.01
150 44 0.08
151 1 0.00
154 68 0.13
155 5 0.01
156 1 0.00
158 27 0.05
159 40 0.08
160 2 0.00
161 1 0.00
163 2 0.00
165 1 0.00
167 8 0.02
168 321 0.61
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (167 bp):
CCTTGAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTAT
TGGCAGATACCCTTTTAGCCTTGAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCG
AACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTG
Found at i:739488 original size:252 final size:249
Alignment explanation
Indices: 739115--739946 Score: 836
Period size: 252 Copynumber: 3.4 Consensus size: 249
739105 ACCCTTATCT
* * *
739115 CCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAATCAAACTCGAAGGTCTTTTAT
1 CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTAT
** * * * * * * * *
739180 TTTCAGATGACCCTT-TTAGCCCTGAGCTATACTACAAATGTTATGCCTTTGAGCTGAGCGTAGT
66 TGGCAGATAACCCTTCTT-TCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGT
739244 CGAACTCGAAGGTTTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTG
130 CGAACTCGAAGG-TTTTT-TTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTG
* * * *
739309 CCTTTGAGCTAAGCGTAGTAGAACTCGAAGGCCTTTTGTTGGCAGATAACCCTTCTAG
193 CCTTTGAGCTGAGCGTAGTCGAACTCGAAGG-CTTTTGTTGGCAGATAGCCCTTCTTG
* * *
739367 CCTTGAGTTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
1 CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTAT
* * * *
739432 TGGAAAATAACCCTTCTTTCCTTGAGATATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
66 TGGCAGATAACCCTTCTTTCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTC
* * * * * * *
739497 GAACTCGAAGGTCTTTTATTGGCAGATAACCTTTCTAGCCTTGAGTTATATTGCAAATGATATGC
131 GAACTCGAAGGT-TTTT-TTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGC
*
739562 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGC-GAATAGCCCTTCTTG
194 CTTTGAGCTGAGCGTAGTCGAACTCGAAGG-CTTTTGTTGGCAG-ATAGCCCTTCTTG
* * * *
739619 CCCTGAGTTATGTTGCAAATAATGTGCCTTGAAGCTGA--G----CG---T---A--TCTTTTAT
1 CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTAT
* * * * * *
739670 TGGCAGATAACCCTTCTATCCTTGAGTTATGCTGGAAATGATGTTCCTTTGAGCTGAGTGTAATC
66 TGGCAGATAACCCTTCTTTCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTC
* * * * *
739735 GAACTCCAAGG--TCTTTGGCAAATAGGCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCC-
131 GAACTCGAAGGTTTTTTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
* * * *
739797 TTGAGCTGAGTGTAATCGAATTCGAAGG--TCT-TTGGCAGATAGCCCTTCTTG
196 TTGAGCTGAGCGTAGTCGAACTCGAAGGCTTTTGTTGGCAGATAGCCCTTCTTG
* * * * * * *
739848 CCTTAAGCTATGCTGAAAATGATTTGCCTT-GAGCTGAGTGTAATCGAAGTTGAAGGTC---T-T
1 CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTAT
* * ** *
739908 CGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
66 TGGCAGATAACCCTTCTTTCCTTGAGATATGCTGCAAAT
739947 AGTTTTTTTT
Statistics
Matches: 483, Mismatches: 79, Indels: 50
0.79 0.13 0.08
Matches are distributed among these distances:
228 6 0.01
229 41 0.08
230 4 0.01
233 24 0.05
234 40 0.08
235 2 0.00
237 1 0.00
238 108 0.22
239 1 0.00
240 2 0.00
242 2 0.00
243 1 0.00
246 2 0.00
250 1 0.00
251 2 0.00
252 244 0.51
253 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (249 bp):
CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTAT
TGGCAGATAACCCTTCTTTCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTC
GAACTCGAAGGTTTTTTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCT
TTGAGCTGAGCGTAGTCGAACTCGAAGGCTTTTGTTGGCAGATAGCCCTTCTTG
Found at i:739725 original size:70 final size:70
Alignment explanation
Indices: 739592--739727 Score: 161
Period size: 70 Copynumber: 1.9 Consensus size: 70
739582 AACTCGAAGG
* * *
739592 TCTTTTGTTGGCGAATAGCCCTTCTTGCCCTGAGTTATGTTGCAAATAATGTGCCTTGAAGCTGA
1 TCTTTTATTGGCGAATAACCCTTCTTGCCCTGAGTTATGCTGCAAATAATGTGCCTTGAAGCTGA
739657 GCGTA
66 GCGTA
* * * *
739662 TCTTTTATTGGC-AGATAACCCTTCTAT-CCTTGAGTTATGCTGGAAATGATGTTCCTTTG-AGC
1 TCTTTTATTGGCGA-ATAACCCTTCT-TGCCCTGAGTTATGCTGCAAATAATGTGCC-TTGAAGC
739724 TGAG
63 TGAG
739728 TGTAATCGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
69 1 0.02
70 51 0.91
71 4 0.07
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (70 bp):
TCTTTTATTGGCGAATAACCCTTCTTGCCCTGAGTTATGCTGCAAATAATGTGCCTTGAAGCTGA
GCGTA
Found at i:739828 original size:79 final size:79
Alignment explanation
Indices: 739669--739946 Score: 362
Period size: 79 Copynumber: 3.5 Consensus size: 79
739659 GTATCTTTTA
* * * * *
739669 TTGGCAGATAACCCTTCTAT-CCTTGAGTTATGCTGGAAATGATGTTCCTTTGAGCTGAGTGTAA
1 TTGGCAGATAGCCCTTCT-TGCCTTAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGTGTAA
* *
739733 TCGAACTCCAAGGTCT
64 TCGAATTCGAAGGTCT
* *
739749 TTGGCAAATAGGCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATC
1 TTGGCAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATC
739814 GAATTCGAAGGTCT
66 GAATTCGAAGGTCT
* *
739828 TTGGCAGATAGCCCTTCTTGCCTTAAGCTATGCTGAAAATGATTTGCCTTGAGCTGAGTGTAATC
1 TTGGCAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATC
739893 GAAGTT-GAAGGTCT
66 GAA-TTCGAAGGTCT
* * * * * *
739907 TCGGTAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 TTGGCAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAAT
739947 AGTTTTTTTT
Statistics
Matches: 176, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
79 135 0.77
80 41 0.23
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (79 bp):
TTGGCAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATC
GAATTCGAAGGTCT
Found at i:741276 original size:95 final size:95
Alignment explanation
Indices: 741062--741323 Score: 321
Period size: 95 Copynumber: 2.7 Consensus size: 95
741052 GGCAAGCTGA
* * * * *
741062 ATCCATAAAGTCAGGGCGCTTAACCAATTGCTCTAGAGGGACAACTTAA--TATCATTGTATAGA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCT-TTATTGTAT---
* *
741125 CATTACAATCACCTTTATCAGGCTAGGTGAATATT
62 -ATTATAACCACCTTTATCAGGCTAGGTGAATATT
* *
741160 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
* * *
741225 TAACCACCTTTATCAGGCTAGTTGGATCTT
66 TAACCACCTTTATCAGGCTAGGTGAATATT
* * *
741255 ATCCATAAAGCCAGAGCGTTTAACCAATTGCTTTAGAGGGATAATTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATAT-T
741320 ATAA
65 ATAA
741324 TATTATAATC
Statistics
Matches: 144, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
95 87 0.60
96 5 0.03
98 43 0.30
99 8 0.06
100 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
TAACCACCTTTATCAGGCTAGGTGAATATT
Found at i:743911 original size:7 final size:7
Alignment explanation
Indices: 743899--743930 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
743889 AAACTAAAGA
743899 AAAAATT
1 AAAAATT
743906 AAAAATT
1 AAAAATT
743913 AAAAAATT
1 -AAAAATT
743921 AAAAATT
1 AAAAATT
743928 AAA
1 AAA
743931 TAAGTTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAAATT
Found at i:743918 original size:15 final size:15
Alignment explanation
Indices: 743898--743930 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
743888 CAAACTAAAG
743898 AAAAAATTAAAAATT
1 AAAAAATTAAAAATT
743913 AAAAAATTAAAAATT
1 AAAAAATTAAAAATT
743928 AAA
1 AAA
743931 TAAGTTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAAATTAAAAATT
Found at i:743976 original size:14 final size:15
Alignment explanation
Indices: 743943--743996 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
743933 AGTTGGAAAA
743943 AATAAATAAAAAATG
1 AATAAATAAAAAATG
*
743958 AATAAGTAAAAAATG
1 AATAAATAAAAAATG
743973 -ATAAAT-AAAAATAG
1 AATAAATAAAAAAT-G
743987 AATAAA-AAAA
1 AATAAATAAAA
743997 GTTAAAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 6 0.18
14 6 0.18
15 22 0.65
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (15 bp):
AATAAATAAAAAATG
Found at i:745114 original size:3 final size:3
Alignment explanation
Indices: 745106--745144 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
745096 TGGACCCCTA
745106 AAT AAT AAT AAT AA- AAT AAT AAT AA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
745145 ATAAATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:745125 original size:11 final size:11
Alignment explanation
Indices: 745109--745173 Score: 75
Period size: 11 Copynumber: 6.2 Consensus size: 11
745099 ACCCCTAAAT
745109 AATAATAATAA
1 AATAATAATAA
745120 AATAATAATAA
1 AATAATAATAA
745131 AATAATAATAA
1 AATAATAATAA
*
745142 TA-AATAAATAA
1 AATAAT-AATAA
*
745153 AAAAATAA-AA
1 AATAATAATAA
745163 AA-AATAA-AA
1 AATAATAATAA
745172 AA
1 AA
745174 AATGTTTTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
9 9 0.18
10 7 0.14
11 31 0.62
12 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AATAATAATAA
Found at i:745137 original size:25 final size:26
Alignment explanation
Indices: 745105--745176 Score: 94
Period size: 25 Copynumber: 2.8 Consensus size: 26
745095 TTGGACCCCT
*
745105 AAATAATAATAATAAAAT-AATAATA
1 AAATAATAATAATAAAATAAATAAAA
745130 AAATAATAATAAT-AAATAAATAAAA
1 AAATAATAATAATAAAATAAATAAAA
* * *
745155 AAATAAAAAAAATAAAAAAAAT
1 AAATAATAATAATAAAATAAAT
745177 GTTTTCAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
24 4 0.10
25 30 0.73
26 7 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (26 bp):
AAATAATAATAATAAAATAAATAAAA
Found at i:745263 original size:30 final size:30
Alignment explanation
Indices: 745227--745330 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
745217 ATATATATTA
*
745227 TATATATGTTTTCAAAA-ATATTTCAAAAAT
1 TATATATGTTTTCAAAATAT-TTTCAAAAAC
745257 TATATATGTTTTCAAAATATTTTCAAAAAC
1 TATATATGTTTTCAAAATATTTTCAAAAAC
*
745287 TATACAACATATGTTTTCAAAAAATGTTTTCAAAAAC
1 TAT-----ATATGTTTTC--AAAATATTTTCAAAAAC
745324 TATATAT
1 TATATAT
745331 TATATATATT
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
30 29 0.45
31 2 0.03
32 4 0.06
35 10 0.16
37 19 0.30
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (30 bp):
TATATATGTTTTCAAAATATTTTCAAAAAC
Found at i:745315 original size:13 final size:13
Alignment explanation
Indices: 745297--745322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
745287 TATACAACAT
745297 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
745310 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
745323 CTATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATGTTTTCAAAAA
Found at i:745328 original size:106 final size:104
Alignment explanation
Indices: 745199--745435 Score: 270
Period size: 106 Copynumber: 2.2 Consensus size: 104
745189 TTATTTAAAG
* *
745199 AAAAATGTTTTTCAAAAAATATATATTATATATATGTTTTCAAAA-ATA-TTTCAAAAA-T-TAT
1 AAAAATG-TTTTCAAAAACTATATATTATATATA--TTTT-AAAATATATTTTAAAAAACTATAT
*
745260 ATAT-GTTTTCAAAATATTTTCAAAAACTATACAACATATGTTTT
62 ATATGGTTTTCAAAA-ATTTTC-AAAACTATACAACATATATTTT
745304 CAAAAAATGTTTTCAAAAACTATATATTATATATATTTTAAAATATATTTTTTAAAAAACTATAT
1 --AAAAATGTTTTCAAAAACTATATATTATATATATTTTAAAATATA--TTTTAAAAAACTATAT
* * *
745369 ATATGGTTTTTAAAAATTTTCAAAACTATATAATATATATTTT
62 ATATGGTTTTCAAAAATTTTCAAAACTATACAACATATATTTT
**
745412 TGAAATGTTTTC-AAAACTATATAT
1 AAAAATGTTTTCAAAAACTATATAT
745436 ATTCGAAAAT
Statistics
Matches: 115, Mismatches: 8, Indels: 16
0.83 0.06 0.12
Matches are distributed among these distances:
103 4 0.03
104 7 0.06
105 12 0.10
106 35 0.30
107 15 0.13
108 20 0.17
109 13 0.11
110 9 0.08
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (104 bp):
AAAAATGTTTTCAAAAACTATATATTATATATATTTTAAAATATATTTTAAAAAACTATATATAT
GGTTTTCAAAAATTTTCAAAACTATACAACATATATTTT
Found at i:745394 original size:31 final size:33
Alignment explanation
Indices: 745359--745437 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 33
745349 TATTTTTTAA
*
745359 AAAACTATATATAT-GGTTTTT-AAAAATTTTC
1 AAAACTATATATATAGATTTTTGAAAAATTTTC
* **
745390 AAAACTATATAATATATATTTTTGAAATGTTTTC
1 AAAACTATAT-ATATAGATTTTTGAAAAATTTTC
745424 AAAACTATATATAT
1 AAAACTATATATAT
745438 TCGAAAATCG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 10 0.24
32 4 0.10
33 9 0.22
34 18 0.44
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (33 bp):
AAAACTATATATATAGATTTTTGAAAAATTTTC
Found at i:745432 original size:27 final size:30
Alignment explanation
Indices: 745400--745468 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
745390 AAAACTATAT
745400 AATATATATTTTTG-AAAT-GTTTTC-AAA
1 AATATATATTTTTGAAAATCGTTTTCTAAA
* * *
745427 ACTATATATATTCGAAAATCGTTTTCTAAA
1 AATATATATTTTTGAAAATCGTTTTCTAAA
745457 AAT-TATATTTTT
1 AATATATATTTTT
745469 TTCAAAAACA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 11 0.33
28 4 0.12
29 13 0.39
30 5 0.15
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (30 bp):
AATATATATTTTTGAAAATCGTTTTCTAAA
Found at i:746129 original size:78 final size:78
Alignment explanation
Indices: 746000--746211 Score: 311
Period size: 78 Copynumber: 2.7 Consensus size: 78
745990 ACAAAAAAAA
* * *
746000 TTATTAAGTTTCAAGTTGAATTAAACACAAATCAAATAATTTCCTAATAAAATTGAATACCACTC
1 TTATTAAGTATCAAGTTGAATCAAACACAAATCAAATAATTTTCTAATAAAATTGAATACCACTC
746065 GTCTCCATAAATT
66 GTCTCCATAAATT
* **
746078 TTATTAAATATCAAGTTGAATCAAACACAAATCAAATAATTTTCTAATAAAATTGAATATTACTC
1 TTATTAAGTATCAAGTTGAATCAAACACAAATCAAATAATTTTCTAATAAAATTGAATACCACTC
*
746143 GTCTCCGTAAATT
66 GTCTCCATAAATT
* * * *
746156 TTATTAAGTATCAAG-TAAATCGAACA-AAGTCAAATATTTTTCTAATAAAATTGAAT
1 TTATTAAGTATCAAGTTGAATCAAACACAAATCAAATAATTTTCTAATAAAATTGAAT
746212 TTACTCGTCT
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
76 28 0.23
77 9 0.07
78 85 0.70
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (78 bp):
TTATTAAGTATCAAGTTGAATCAAACACAAATCAAATAATTTTCTAATAAAATTGAATACCACTC
GTCTCCATAAATT
Found at i:746792 original size:183 final size:183
Alignment explanation
Indices: 746470--746858 Score: 589
Period size: 183 Copynumber: 2.1 Consensus size: 183
746460 GATACAAATA
* * *
746470 AAAAATGTATCGATCCATAGCCATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
** * *
746535 AAACCGGTAAAGCGCTATCGGATATATTGAAAGTATCGATTAGATTGAAATAAATATCGATACTT
66 AAACCGGTAAAGCAATACCGGATATATTGAAAGTATCGATTAGATTGAAATAAATATCGACACTT
* * * * *
746600 TTGGAATTTAAAAGAGAAGAAGTAATAACGCCTATAAAGTATCGATATTTTAT
131 TTAGAATTTAAAAGAGAAGAAGTAATAACACCTATAAAATATCGACACTTTAT
* *
746653 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAACCCGGTCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* * **
746718 AAATCGGTAAAGCAATACCGGATATGTTGAAAGTATCGATTAGATTGAAATATGTATCGACACTT
66 AAACCGGTAAAGCAATACCGGATATATTGAAAGTATCGATTAGATTGAAATAAATATCGACACTT
* *
746783 TTAGAATTTAAAAGAGAAGAAGTAATAGCACCTATAAAATGTCGACACTTTAT
131 TTAGAATTTAAAAGAGAAGAAGTAATAACACCTATAAAATATCGACACTTTAT
*
746836 AAAAATGTATCGATCTATAACAA
1 AAAAATGTATCGATCCATAACAA
746859 CATGCTTGAG
Statistics
Matches: 185, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
183 185 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.26
Consensus pattern (183 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGACA
AAACCGGTAAAGCAATACCGGATATATTGAAAGTATCGATTAGATTGAAATAAATATCGACACTT
TTAGAATTTAAAAGAGAAGAAGTAATAACACCTATAAAATATCGACACTTTAT
Found at i:747681 original size:198 final size:199
Alignment explanation
Indices: 747215--747686 Score: 596
Period size: 200 Copynumber: 2.4 Consensus size: 199
747205 GTAAACATAT
* *
747215 GTGTCGATACATTTTATAAAAGTATCGA-CCCAAAAAACATCGAAACCACTAATTATAATGTAAT
1 GTGTCGATACA-TTTATAAAAGTATCGATCCC-AAAAACATCGAAACTAATAATTATAATGTAAT
* * * *
747279 ATGTAAATTAACAATGTAACCGATATAAATATACCGGTTAATTACAAAACATGTCAACACAATGT
64 AGGTAAATTTACAATGTAACCGATATAAATATACCGGTTAATGACAAAACATCTCAACACAATGT
** * *
747344 ATTGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACG
129 ATCAACACTTGTGGAATTTGAGTCGAAACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACG
747409 CATAAA
194 CATAAA
* * *
747415 GTGCCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAA-TCGATAATTATAATATAAT
1 GTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACT-AATAATTATAATGTAAT
* * * * *
747479 AGGTAAATTTACAATGTAACC-AGTATAAATATACCGGTTTTATGAGAGAATATCTCAACATAAT
64 AGGTAAATTTACAATGTAACCGA-TATAAATATACCGG-TTAATGACAAAACATCTCAACACAAT
* *** * * *
747543 GTATCAACACTTTTTTTATTTGAGTCGAAACTT-TTTTCTAGAATGAATGTCC-AACGAGGTGCA
127 GTATCAACACTTGTGGAATTTGAGTCGAAACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCA
*
747606 TGCATAAA
192 CGCATAAA
*
747614 GTGTCGATACATTTA-AAATTGTATCGATCCCAAAAACATCGAAACTAATAATTATAATGTAATA
1 GTGTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACTAATAATTATAATGTAATA
747678 GGTAAATTT
65 GGTAAATTT
747687 GTAATATTAC
Statistics
Matches: 235, Mismatches: 30, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
197 3 0.01
198 49 0.21
199 38 0.16
200 98 0.42
201 47 0.20
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (199 bp):
GTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACTAATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGATATAAATATACCGGTTAATGACAAAACATCTCAACACAATGTAT
CAACACTTGTGGAATTTGAGTCGAAACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCACGCA
TAAA
Found at i:747833 original size:87 final size:87
Alignment explanation
Indices: 747734--747972 Score: 354
Period size: 87 Copynumber: 2.7 Consensus size: 87
747724 AAATAGGTCA
*
747734 ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
747799 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* * * *
747821 ATATAAGCGCTACTTATTACATTATATAAGAGCTACTTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
747886 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* * * * * * *
747908 TTATAAGCACTACCTATTACACTATATAAACGTTACAC-AATATTTTATTGTAATTGATAATATT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTAC-CTAATATGTTATTGTACTTGATAATATT
747972 T
65 T
747973 GTTAAATGAT
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
87 135 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Done.