Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005690.1 Hibiscus syriacus cultivar Beakdansim tig00013311_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: 64822
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1577 original size:20 final size:20
Alignment explanation
Indices: 1532--1740 Score: 160
Period size: 20 Copynumber: 11.2 Consensus size: 20
1522 TTACACATTC
*
1532 ATTTGAATATCGC-ACGCGA
1 ATTTGACTATCGCAACGCGA
1551 A-TTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1570 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1590 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
1609 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1624 A-TTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
1643 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
* *
1663 ATTTGACTATCGCAAACGGGT
1 ATTTGACTATCGC-AACGCGA
** *
1684 ATTCAACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1704 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
1718 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1738 ATT
1 ATT
1741 GAATTTCTCG
Statistics
Matches: 155, Mismatches: 20, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
14 19 0.12
15 3 0.02
16 1 0.01
18 12 0.08
19 22 0.14
20 80 0.52
21 18 0.12
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1667 original size:73 final size:72
Alignment explanation
Indices: 1540--1677 Score: 222
Period size: 73 Copynumber: 1.9 Consensus size: 72
1530 TCATTTGAAT
*
1540 ATCGCACGCGAATTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAA
1 ATCGCACGCGAATTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAA
1605 CTCAAAA
66 CTCAAAA
* * * *
1612 ATCGCAACGCGAATTGACTATCGCAACGTGAATTTGATTATCGCAACGGGTATTTGACTATCGCA
1 ATCGC-ACGCGAATTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCA
1677 A
65 A
1678 ACGGGTATTC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
72 5 0.08
73 55 0.92
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (72 bp):
ATCGCACGCGAATTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAA
CTCAAAA
Found at i:1933 original size:13 final size:14
Alignment explanation
Indices: 1874--1933 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 14
1864 CACAAATAAG
*
1874 AATTATTTACACATC
1 AATT-TTTACAAATC
**
1889 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
1904 AA-CTTTACAAATC
1 AATTTTTACAAATC
1917 AATTTTTAC-AATC
1 AATTTTTACAAATC
1930 AATT
1 AATT
1934 AACAAGCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
13 18 0.50
14 5 0.14
15 12 0.33
16 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:3949 original size:20 final size:20
Alignment explanation
Indices: 3924--3999 Score: 118
Period size: 20 Copynumber: 3.8 Consensus size: 20
3914 TCGCAACACG
*
3924 AATGACTATTGCAACGCGAA
1 AATGACTATCGCAACGCGAA
3944 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
3964 AATGACTATCGCAACGC-AA
1 AATGACTATCGCAACGCGAA
*
3983 ATTTGACTATCGCAACG
1 A-ATGACTATCGCAACG
4000 AGAGAATCGC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 3 0.06
20 50 0.94
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:4069 original size:20 final size:20
Alignment explanation
Indices: 4044--4089 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
4034 GATTCTTTCA
4044 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
**
4064 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCG
4084 TTGCGA
1 TTGCGA
4090 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:4254 original size:18 final size:18
Alignment explanation
Indices: 4231--4280 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
4221 TTTACTAAGC
*
4231 AATCTAATTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
4249 AATCTAAGTAAAATGGTT
1 AATCTAAGTGAAATGGTT
*
4267 AATATAAGTGAAAT
1 AATCTAAGTGAAAT
4281 TACGAGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.34
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:6050 original size:20 final size:20
Alignment explanation
Indices: 6001--6068 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
5991 TCTGAAACTT
*
6001 AAAATCGCAACACAAAAATA
1 AAAATCGCAACACGAAAATA
* *
6021 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACGAAAATA
** * *
6041 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATA
6060 AAAATCGCA
1 AAAATCGCA
6069 TTGCGATTCT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 7 0.18
20 31 0.82
ACGTcount: A:0.53, C:0.22, G:0.12, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATA
Found at i:6679 original size:20 final size:20
Alignment explanation
Indices: 6650--6707 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
6640 CGCTTTGAAA
*
6650 ATCGCATTGCGATAGTCAAC
1 ATCGCGTTGCGATAGTCAAC
*
6670 ATCGCGTTGCGATAGTCAGC
1 ATCGCGTTGCGATAGTCAAC
6690 ATCGCGTTGCGATAGTCA
1 ATCGCGTTGCGATAGTCA
6708 TATTCGCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAC
Found at i:6714 original size:20 final size:20
Alignment explanation
Indices: 6651--6741 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
6641 GCTTTGAAAA
*
6651 TCGCATTGCGATAGTCA-ACA
1 TCGCATTGCGATAGTCATA-T
* *
6671 TCGCGTTGCGATAGTCAGCA-
1 TCGCATTGCGATAGTCA-TAT
*
6691 TCGCGTTGCGATAGTCATAT
1 TCGCATTGCGATAGTCATAT
*
6711 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGT-CATAT
6731 TCGCATTGCGA
1 TCGCATTGCGA
6742 ATTCGGAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.03
20 60 0.95
22 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATAT
Found at i:6762 original size:21 final size:21
Alignment explanation
Indices: 6738--6783 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
6728 TATTCGCATT
6738 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
6759 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
6780 GCGA
1 GCGA
6784 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:8659 original size:174 final size:176
Alignment explanation
Indices: 8447--8808 Score: 570
Period size: 175 Copynumber: 2.1 Consensus size: 176
8437 ATAAAAATTA
* * *
8447 AATATTTTTTAATTCAAAAAAACAGTTTCTAATTAATTTAAATAATATCTAATTATAAAATATAA
1 AATA-TTTTTAATTAAAAAAAACAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAA
8512 ATTTTATATAAA-TTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
65 ATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
* *
8576 ATTAATTGGATTTTAAAAGGTTTGGGCTGAGC-CTATATATTATATAT
130 ATTAATTAGATTTTAAAAGATTTGGGCTGAGCTC-ATATATTATATAT
* *
8623 AATATTTTTAATTAAAAAAAATA-TTTAC-AATTAATTTAAATTATATATAATTATAAAATAAAA
1 AATATTTTTAATTAAAAAAAACAGTTT-CTAATTAATTTAAATAATATATAATTATAAAATAAAA
8686 ATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
65 ATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
* * *
8751 ATTAATTAGATTTTAAATGATTTGGGTTGAGCTCATATGTTATATAT
130 ATTAATTAGATTTTAAAAGATTTGGGCTGAGCTCATATATTATATAT
*
8798 AATATATTTAA
1 AATATTTTTAA
8809 AATTTAAAAT
Statistics
Matches: 172, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
174 47 0.27
175 120 0.70
176 5 0.03
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (176 bp):
AATATTTTTAATTAAAAAAAACAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAA
TTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTA
TTAATTAGATTTTAAAAGATTTGGGCTGAGCTCATATATTATATAT
Found at i:15140 original size:3 final size:3
Alignment explanation
Indices: 15134--15211 Score: 81
Period size: 3 Copynumber: 26.0 Consensus size: 3
15124 AATATAATAT
* * *
15134 TTA TTA TTA TTCA -TA CTA TTA -AA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15178 TTA TTA TTA TTA TGT- TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA
15212 ATACAAGTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
2 3 0.05
3 56 0.88
4 5 0.08
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:16700 original size:29 final size:28
Alignment explanation
Indices: 16668--16737 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
16658 TTACTTATTA
*
16668 TTTTTACTATTTAATCCTTTAAGAT-TCT-
1 TTTTTACTATTTAATCCCTTAA-ATGT-TG
*
16696 TTTTTACTGTTTTAATCCCTTAAATGTTTG
1 TTTTTACT-ATTTAATCCCTTAAATG-TTG
16726 TTTTTACTATTT
1 TTTTTACTATTT
16738 TAGACCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 10 0.29
29 16 0.46
30 9 0.26
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (28 bp):
TTTTTACTATTTAATCCCTTAAATGTTG
Found at i:16758 original size:30 final size:30
Alignment explanation
Indices: 16668--16828 Score: 116
Period size: 30 Copynumber: 5.4 Consensus size: 30
16658 TTACTTATTA
*
16668 TTTTTACTA-TTTA-ATCCTTTAAGATTCT-
1 TTTTTACTATTTTAGA-CCTTTAAGTTTCTG
* * *
16696 TTTTTACTGTTTTA-ATCCCTTAAATGTT-TG
1 TTTTTACTATTTTAGA-CCTTTAAGT-TTCTG
*
16726 TTTTTACTATTTTAGACCTTTAAGTTTATG
1 TTTTTACTATTTTAGACCTTTAAGTTTCTG
* * * *
16756 TTTATGCTATTTTAGCCCTTTAGGTTTCTG
1 TTTTTACTATTTTAGACCTTTAAGTTTCTG
** ** * *
16786 TTTTTGTTATTTTAGTGCTTTAAATTCCTG
1 TTTTTACTATTTTAGACCTTTAAGTTTCTG
*
16816 TTTGTACTATTTT
1 TTTTTACTATTTT
16829 GGTCCTTTGG
Statistics
Matches: 106, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
28 8 0.08
29 15 0.14
30 82 0.77
31 1 0.01
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.58
Consensus pattern (30 bp):
TTTTTACTATTTTAGACCTTTAAGTTTCTG
Found at i:18732 original size:30 final size:30
Alignment explanation
Indices: 18696--18756 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
18686 TTGTCTTACA
*
18696 TGTACTAAATAATTTCTTTTCTTTTGTTTG
1 TGTACTAAATAATTTCTTTTCTGTTGTTTG
* *
18726 TGTACTAATTTATTTCTTTTCTGTTGTTTG
1 TGTACTAAATAATTTCTTTTCTGTTGTTTG
18756 T
1 T
18757 ATCATTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.10, G:0.11, T:0.62
Consensus pattern (30 bp):
TGTACTAAATAATTTCTTTTCTGTTGTTTG
Found at i:20845 original size:21 final size:21
Alignment explanation
Indices: 20821--20874 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
20811 AACAAAGGTA
*
20821 GTACTGATACCCTTTGAAGGG
1 GTACCGATACCCTTTGAAGGG
20842 GTACCGATACCCTTTGAAGGG
1 GTACCGATACCCTTTGAAGGG
20863 GTACCGATACCC
1 GTACCGATACCC
20875 CCTGTTCTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (21 bp):
GTACCGATACCCTTTGAAGGG
Found at i:20941 original size:20 final size:21
Alignment explanation
Indices: 20903--20942 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20893 TTTTTGCAGA
*
20903 CAAATTATCCCCAAACGGCTC
1 CAAAATATCCCCAAACGGCTC
20924 CAAAATATCCCC-AACGGCT
1 CAAAATATCCCCAAACGGCT
20943 ATATACGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.35, C:0.38, G:0.10, T:0.17
Consensus pattern (21 bp):
CAAAATATCCCCAAACGGCTC
Found at i:23546 original size:22 final size:22
Alignment explanation
Indices: 23484--23562 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
23474 AGAGATATTG
*
23484 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAAAGGGTATCA
* * *
23506 ATACCTCTTATGAACGGGTATCG
1 ATACC-CCTATGAAAGGGTATCA
23529 ATACCCCTATGAAAGGGTATCA
1 ATACCCCTATGAAAGGGTATCA
23551 ATACCCC-ATGAA
1 ATACCCCTATGAA
23563 GGCTCAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.10
22 26 0.52
23 19 0.38
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (22 bp):
ATACCCCTATGAAAGGGTATCA
Found at i:24397 original size:36 final size:35
Alignment explanation
Indices: 24356--24448 Score: 111
Period size: 35 Copynumber: 2.6 Consensus size: 35
24346 TTAAGGAAAA
*
24356 AAACAAAGAGCAAAAAGAA-AAAAAGCAAAGAAAATG
1 AAACAAAGAG-AAAAA-AAGAAAAAACAAAGAAAATG
24392 AAACAAAGAGAAAAAAAGAAAAAACAAAGAAAA--
1 AAACAAAGAGAAAAAAAGAAAAAACAAAGAAAATG
*
24425 AAAGCAAAGAAAAAACAAAGAAAA
1 AAA-CAAAGAGAAAA-AAAGAAAA
24449 TAGTAAAGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
33 3 0.06
34 12 0.23
35 27 0.52
36 10 0.19
ACGTcount: A:0.77, C:0.08, G:0.14, T:0.01
Consensus pattern (35 bp):
AAACAAAGAGAAAAAAAGAAAAAACAAAGAAAATG
Found at i:24400 original size:14 final size:13
Alignment explanation
Indices: 24369--24461 Score: 78
Period size: 13 Copynumber: 7.7 Consensus size: 13
24359 CAAAGAGCAA
24369 AAAGAAAAAAAGC
1 AAAGAAAAAAAGC
24382 AAAGAAAATGAAA-C
1 AAAGAAAA--AAAGC
*
24396 AAAG-AGAAAA--
1 AAAGAAAAAAAGC
24406 AAAG-AAAAAA-C
1 AAAGAAAAAAAGC
24417 AAAGAAAAAAAGC
1 AAAGAAAAAAAGC
24430 AAAG-AAAAAA-C
1 AAAGAAAAAAAGC
* *
24441 AAAG-AAAATAGT
1 AAAGAAAAAAAGC
24453 AAAGAAAAA
1 AAAGAAAAA
24462 GGATACAAGA
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
10 9 0.13
11 17 0.25
12 16 0.23
13 19 0.28
14 5 0.07
15 3 0.04
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAAAGC
Found at i:24426 original size:19 final size:19
Alignment explanation
Indices: 24353--24428 Score: 68
Period size: 19 Copynumber: 4.0 Consensus size: 19
24343 AAGTTAAGGA
*
24353 AAAAAACAAAGAGCAAAAAG
1 AAAAAACAAAGA-AAAAAAG
*
24373 AAAAAAAGCAAAG--AAAATG
1 -AAAAAA-CAAAGAAAAAAAG
* *
24392 AAACAA-AGAGAAAAAAAG
1 AAAAAACAAAGAAAAAAAG
24410 AAAAAACAAAGAAAAAAAG
1 AAAAAACAAAGAAAAAAAG
24429 CAAAGAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
16 3 0.07
18 15 0.33
19 16 0.36
21 6 0.13
22 5 0.11
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.01
Consensus pattern (19 bp):
AAAAAACAAAGAAAAAAAG
Found at i:24433 original size:24 final size:23
Alignment explanation
Indices: 24369--24461 Score: 100
Period size: 24 Copynumber: 3.9 Consensus size: 23
24359 CAAAGAGCAA
24369 AAAGAAAAAAAGCAAAGAAAATGAAAC
1 AAAG-AAAAAAGCAAAG-AAA--AAAC
*
24396 AAAGAGAAAA--AAAGAAAAAAC
1 AAAGAAAAAAGCAAAGAAAAAAC
24417 AAAGAAAAAAAGCAAAGAAAAAAC
1 AAAG-AAAAAAGCAAAGAAAAAAC
* *
24441 AAAGAAAATAGTAAAGAAAAA
1 AAAGAAAAAAGCAAAGAAAAA
24462 GGATACAAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
21 8 0.14
22 5 0.08
23 18 0.31
24 19 0.32
26 5 0.08
27 4 0.07
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.03
Consensus pattern (23 bp):
AAAGAAAAAAGCAAAGAAAAAAC
Found at i:26829 original size:19 final size:19
Alignment explanation
Indices: 26775--26829 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
26765 AACCAATAAT
26775 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
26794 GATGAAA-AAAATGAAATTG
1 AATAAAATAAAAT-AAATTG
26813 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
26830 GAAGATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 5 0.17
18 1 0.03
19 18 0.62
20 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:26936 original size:21 final size:22
Alignment explanation
Indices: 26904--27053 Score: 68
Period size: 22 Copynumber: 6.9 Consensus size: 22
26894 TAATAAGAGC
26904 AAATAAACTAAAAATATAATG-A
1 AAATAAA-TAAAAATATAATGTA
* *
26926 AAATAAATAAATAGTATAA-ATA
1 AAATAAATAAA-AATATAATGTA
* *
26948 AAAT-CATATAAAATAT-ATATA
1 AAATAAATA-AAAATATAATGTA
*
26969 AAAT--ATAAAAATGT-ATGTA
1 AAATAAATAAAAATATAATGTA
*
26988 TAATATAAT-AAAATACTAAATAGTA
1 AAATA-AATAAAAATA-T-AAT-GTA
*
27013 ATAAT-AATAATAAATA-AATGAA
1 A-AATAAATAA-AAATATAATGTA
* *
27035 AAATAAATATACATATAAT
1 AAATAAATAAAAATATAAT
27054 ATTAACTAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 32
0.69 0.08 0.22
Matches are distributed among these distances:
19 13 0.13
20 4 0.04
21 30 0.30
22 33 0.33
23 3 0.03
24 5 0.05
25 4 0.04
26 8 0.08
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (22 bp):
AAATAAATAAAAATATAATGTA
Found at i:27272 original size:22 final size:23
Alignment explanation
Indices: 27231--27273 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
27221 ACGCAAAGAA
27231 AAATGAAAAAAATTATAATAAAT
1 AAATGAAAAAAATTATAATAAAT
27254 AAAT-AAATAAAA-TATAATAA
1 AAATGAAA-AAAATTATAATAA
27274 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
AAATGAAAAAAATTATAATAAAT
Found at i:27273 original size:25 final size:25
Alignment explanation
Indices: 27245--27301 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
27235 GAAAAAAATT
27245 ATAATAAATAAATAAATAAA-ATATA
1 ATAATAAATAAATAAATAAATATA-A
* * * *
27270 ATAATATATATATATATACATATAA
1 ATAATAAATAAATAAATAAATATAA
27295 ATAATAA
1 ATAATAA
27302 GGGTTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAATAAATAAATAAATAAATATAA
Found at i:27734 original size:37 final size:37
Alignment explanation
Indices: 27693--27785 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
27683 ATGCTTGTGG
* * *
27693 ATCCTATCTTTAGGAGTTTAAATAATAATAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTCT
* ** * *
27730 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTCT
27767 ATCCTATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
27786 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTCT
Found at i:28719 original size:106 final size:106
Alignment explanation
Indices: 28534--29791 Score: 1881
Period size: 106 Copynumber: 11.9 Consensus size: 106
28524 CATTGTTTCT
* * * * * ***
28534 AGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGTTCTGGAATCATGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * * *
28599 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
28640 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * *
28705 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
28746 AGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
28811 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
28852 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * *
28917 CAGCGGTCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
28958 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* *
29023 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTGC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
29064 AGTCCAATATCTTTCGATGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
29129 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
29170 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAAGTTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACAA
*
29234 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
29276 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTCTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
29341 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
29382 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * * *
29447 CAGCAGTCCCTTCGTCATGAAGTTGAACTGGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
29488 AGTCCAATATCATTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
29553 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
29594 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * * * *
29659 TAGCAGTCCCTACGTCGTGACGTTGAACTTGCGTTGTATGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
29700 AGTCCAATATCCTTTGTCGTGAAGTTGAAATTGGCTCTGAATTTAGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
29765 CAGTC-GTCCCTTCGTTGTGAAGTTGAA
66 CAG-CGGTCCCTTCGTCGTGAAGTTGAA
29792 ATCCACTCTC
Statistics
Matches: 1056, Mismatches: 93, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
105 5 0.00
106 1047 0.99
107 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:31185 original size:8 final size:8
Alignment explanation
Indices: 31164--31228 Score: 60
Period size: 8 Copynumber: 7.8 Consensus size: 8
31154 TACATGTGCT
31164 TTTTTTTC
1 TTTTTTTC
**
31172 CCTTTTTC
1 TTTTTTTC
31180 -TTTTTTC
1 TTTTTTTC
31187 TTTTTGTTC
1 TTTTT-TTC
31196 TTTTTTTC
1 TTTTTTTC
31204 TTCTTTTTTGC
1 -T-TTTTTT-C
*
31215 TTCTTTTC
1 TTTTTTTC
31223 TTTTTT
1 TTTTTT
31229 ATTTTTTCCC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
7 6 0.13
8 19 0.40
9 14 0.30
10 7 0.15
11 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:31207 original size:11 final size:11
Alignment explanation
Indices: 31187--31235 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
31177 TTCTTTTTTC
*
31187 TTTTTGTTCTT
1 TTTTTCTTCTT
31198 TTTTTCTTCTT
1 TTTTTCTTCTT
*
31209 TTTTGCTTCTT
1 TTTTTCTTCTT
* *
31220 TTCTTTTTTATT
1 TT-TTTCTTCTT
31232 TTTT
1 TTTT
31236 CCCTTTTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 24 0.75
12 8 0.25
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:31207 original size:20 final size:21
Alignment explanation
Indices: 31180--31227 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
31170 TCCCTTTTTC
31180 TTTTTTC-TTTTTG-TTCTTT
1 TTTTTTCTTTTTTGCTTCTTT
31199 TTTTCTTCTTTTTTGCTTCTTT
1 TTTT-TTCTTTTTTGCTTCTTT
31221 TCTTTTT
1 T-TTTTT
31228 TATTTTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.16
20 3 0.12
21 6 0.24
22 9 0.36
23 3 0.12
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (21 bp):
TTTTTTCTTTTTTGCTTCTTT
Found at i:31223 original size:27 final size:27
Alignment explanation
Indices: 31177--31228 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
31167 TTTTCCCTTT
*
31177 TTCTTTTTTCTTTTTGTTCTTTTTTTC
1 TTCTTTTTTCTTCTTGTTCTTTTTTTC
31204 TTCTTTTTTGCTTCTT-TTCTTTTTT
1 TTCTTTTTT-CTTCTTGTTCTTTTTT
31229 ATTTTTTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (27 bp):
TTCTTTTTTCTTCTTGTTCTTTTTTTC
Found at i:35561 original size:20 final size:19
Alignment explanation
Indices: 35511--35566 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
35501 AAACAATAAT
35511 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
35530 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
35550 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
35567 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:35705 original size:21 final size:22
Alignment explanation
Indices: 35660--35750 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 22
35650 AAAATAAATT
*
35660 AATAGTATAAATAAAATAATAAAA
1 AATA-TATATATAAAATAAT-AAA
35684 AATATATATATAAAAT-ATAAA
1 AATATATATATAAAATAATAAA
* * *
35705 AATGTATGTATAATATAAT-AA
1 AATATATATATAAAATAATAAA
*
35726 AATACTAAATAGTAATAATAATAAA
1 AATA-TATATA-TAA-AATAATAAA
35751 TAAATGAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
21 21 0.39
22 8 0.15
23 14 0.26
24 9 0.17
25 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (22 bp):
AATATATATATAAAATAATAAA
Found at i:35988 original size:23 final size:23
Alignment explanation
Indices: 35954--36000 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
35944 ACGCAAAGAA
35954 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
35977 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
36000 A
1 A
36001 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:36727 original size:21 final size:21
Alignment explanation
Indices: 36696--36756 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
36686 TCGAGGGTTC
36696 TACGAGGTCCTTCGGGACATA
1 TACGAGGTCCTTCGGGACATA
* * *
36717 TATGTGGTCCTTCGGGACATC
1 TACGAGGTCCTTCGGGACATA
*
36738 TACGAGGTCCTTTGGGACA
1 TACGAGGTCCTTCGGGACA
36757 ATTTTATATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.28
Consensus pattern (21 bp):
TACGAGGTCCTTCGGGACATA
Found at i:36984 original size:9 final size:9
Alignment explanation
Indices: 36967--37069 Score: 52
Period size: 9 Copynumber: 11.3 Consensus size: 9
36957 ATGACAAAAA
*
36967 GATATTAAT
1 GATAATAAT
36976 GATAATAAT
1 GATAATAAT
*
36985 GTTATATATAT
1 GATA-ATA-AT
36996 GATATGATAAT
1 GATA--ATAAT
*
37007 GATAATGAT
1 GATAATAAT
*
37016 G-T--TAGT
1 GATAATAAT
* *
37022 AATAATAAG
1 GATAATAAT
*
37031 GATCATAAT
1 GATAATAAT
37040 GA-ACATAAT
1 GATA-ATAAT
* *
37049 GAGATTAAT
1 GATAATAAT
37058 GATAATAAT
1 GATAATAAT
37067 GAT
1 GAT
37070 GAGATATGTT
Statistics
Matches: 69, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
6 2 0.03
7 1 0.01
8 1 0.01
9 47 0.68
10 4 0.06
11 11 0.16
12 3 0.04
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.36
Consensus pattern (9 bp):
GATAATAAT
Found at i:38718 original size:65 final size:63
Alignment explanation
Indices: 38583--38736 Score: 215
Period size: 65 Copynumber: 2.4 Consensus size: 63
38573 TATTAGTATC
38583 CTTTGAGT-TGTTTCTCTTGAAACAAATTTTGCCTTTCAAGACAGTTTCTTTTGAAAAAAAAT
1 CTTTGAGTATGTTTCTCTTGAAACAAATTTTGCCTTTCAAGACAGTTTCTTTTGAAAAAAAAT
* * *
38645 CTTTGAGTATGTTTCTCTGGAAACAAAGTTTTGTCTCTT-GAGACAAGTTT-TTTTGAGAAAAAA
1 CTTTGAGTATGTTTCTCTTGAAACAAA-TTTTGCCT-TTCAAGAC-AGTTTCTTTTGA-AAAAAA
38708 AT
62 AT
*
38710 CTTTGAGTATGTTTCCCTTGAAACAAA
1 CTTTGAGTATGTTTCTCTTGAAACAAA
38737 ACAAACATCT
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
62 8 0.10
63 17 0.21
64 17 0.21
65 40 0.49
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (63 bp):
CTTTGAGTATGTTTCTCTTGAAACAAATTTTGCCTTTCAAGACAGTTTCTTTTGAAAAAAAAT
Found at i:38751 original size:65 final size:64
Alignment explanation
Indices: 38621--38751 Score: 149
Period size: 65 Copynumber: 2.0 Consensus size: 64
38611 TTGCCTTTCA
* ******
38621 AGACAGTTTCTTTTGAAAAAAAATCTTTGAGTATGTTTCTCTGGAAACAAAGTTTTGTCTCTTG
1 AGACAGTTTCTTTTGAAAAAAAATCTTTGAGTATGTTTCCCTGGAAACAAACAAACATCTCTTG
*
38685 AGACAAGTTT-TTTTGAGAAAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAACAAACATCT-T
1 AGAC-AGTTTCTTTTGA-AAAAAAATCTTTGAGTATGTTTCCCTGGAAAC-AAACAAACATCTCT
38748 TG
63 TG
38750 AG
1 AG
38752 TCGTTTCCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
64 10 0.18
65 40 0.71
66 6 0.11
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (64 bp):
AGACAGTTTCTTTTGAAAAAAAATCTTTGAGTATGTTTCCCTGGAAACAAACAAACATCTCTTG
Found at i:38961 original size:42 final size:40
Alignment explanation
Indices: 38860--39045 Score: 115
Period size: 40 Copynumber: 4.3 Consensus size: 40
38850 CATGACATCA
38860 TCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCC
1 TCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCC
** ** * * *
38900 TCATCATGTAGGAGTCGTGTCA-CCCCTGATAACCAGTCGTCC
1 TCATCGCGTAGGAACCGTGTCATCCCCCG---ACCAGACCTCC
* *
38942 TCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCATG-CCGTCC
1 TCATCGCGTAGGAACCGTGTCAT--CCC--CC----GA--CCA-GACC-TCC
* *
38993 TCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCC
1 TCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCC
*
39033 TCATCACGTAGGA
1 TCATCGCGTAGGA
39046 GTCATGTCAC
Statistics
Matches: 110, Mismatches: 19, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
39 5 0.05
40 35 0.32
41 4 0.04
42 26 0.24
43 2 0.02
45 3 0.03
47 2 0.02
48 1 0.01
49 3 0.03
50 3 0.03
51 26 0.24
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.23
Consensus pattern (40 bp):
TCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCC
Found at i:39219 original size:131 final size:131
Alignment explanation
Indices: 38839--39231 Score: 495
Period size: 131 Copynumber: 3.0 Consensus size: 131
38829 AACCATTATC
* * *
38839 CCTAAATATGGCATGACATCATCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
1 CCTAAAGATGGCATGACGTCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
* * *
38904 CATGTAGGAGTCGTGTCACCCCT-GATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCGC
66 CACGTAGGAGTCGTGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAATCGTGTTAT---
*
38968 CCTT
128 CATT
* * *
38972 CCTAAAGATGGCATGCCGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCAT
1 CCTAAAGATGGCATGACGTCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
* * ** *
39037 CACGTAGGAGTCATGTCACCCCTAGACAACCTTTCGTCCTCATCACGTAGGAATCGTGTTATCAT
66 CACGTAGGAGTCGTGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAATCGTGTTATCAT
39102 T
131 T
* * * ** *
39103 TCTAAAGATGGCATGTCGTCCTCATCGTGTAGGAACTATGTCATCCCCCGACCAGACCTTCTCAT
1 CCTAAAGATGGCATGACGTCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
* * **
39168 CACGTAGGAG-CTGTGTCACCCCTAGATAATCAATCGTCCTCGTCGTATAGGAAAT-GTGTTATC
66 CACGTAGGAGTC-GTGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGG-AATCGTGTTATC
39231 A
129 A
39232 CCCCTCATAA
Statistics
Matches: 226, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
130 1 0.00
131 109 0.48
132 3 0.01
133 80 0.35
134 33 0.15
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.26
Consensus pattern (131 bp):
CCTAAAGATGGCATGACGTCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCAT
CACGTAGGAGTCGTGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAATCGTGTTATCAT
T
Found at i:39319 original size:134 final size:132
Alignment explanation
Indices: 38840--39327 Score: 493
Period size: 131 Copynumber: 3.7 Consensus size: 132
38830 ACCATTATCC
* * * ** *
38840 CTAAATATGGCATGACATCATCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATC
1 CTAAAGATGGCATGACGTCCTCATCATGTAGGAACCATGTCAT-CCCCGACCAGACCTCCTCATC
* * ** *
38905 ATGTAGGAGTCGTGTCACCCCT-GATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCGCC
65 ACGTAGGAGTCGTGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAAATGTGTTATCACC
38969 CTT
130 CTT
* * *
38972 CCTAAAGATGGCATGCCGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCAT
1 -CTAAAGATGGCATGACGTCCTCATCATGTAGGAACCATGTCATCCC-CGACCAGACCTCCTCAT
* * ** *
39037 CACGTAGGAGTCATGTCACCCCTAGACAACCTTTCGTCCTCATCACGTAGG-AATCGTGTTATCA
64 CACGTAGGAGTCGTGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAAAT-GTGTTATCA
*
39101 --TTT
128 CCCTT
* * * *
39104 CTAAAGATGGCATGTCGTCCTCATCGTGTAGGAACTATGTCATCCCCCGACCAGACCTTCTCATC
1 CTAAAGATGGCATGACGTCCTCATCATGTAGGAACCATGTCAT-CCCCGACCAGACCTCCTCATC
* * **
39169 ACGTAGGAG-CTGTGTCACCCCTAGATAATCAATCGTCCTCGTCGTATAGGAAATGTGTTATCAC
65 ACGTAGGAGTC-GTGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAAATGTGTTATCAC
*
39233 CCCT
129 CCTT
* * * * * * * *
39237 CATAAAGATGGCCATAAC-TCTTCATTATGTATGAGCCATGTTATCCACAGACCAGATCTCCTCA
1 C-TAAAGATGG-CATGACGTCCTCATCATGTAGGAACCATGTCATCC-CCGACCAGACCTCCTCA
** *
39301 TCATATAGGAGTCGTGTCACCCTTAGA
63 TCACGTAGGAGTCGTGTCACCCCTAGA
39328 CGACCAGAAC
Statistics
Matches: 296, Mismatches: 47, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
130 1 0.00
131 103 0.35
132 11 0.04
133 81 0.27
134 95 0.32
135 5 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (132 bp):
CTAAAGATGGCATGACGTCCTCATCATGTAGGAACCATGTCATCCCCGACCAGACCTCCTCATCA
CGTAGGAGTCGTGTCACCCCTAGATAACCAATCGTCCTCATCGCGTAGGAAATGTGTTATCACCC
TT
Found at i:39347 original size:265 final size:264
Alignment explanation
Indices: 38840--39350 Score: 598
Period size: 265 Copynumber: 1.9 Consensus size: 264
38830 ACCATTATCC
* *
38840 CTAAATATGGCATGACATCATCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATC
1 CTAAAGATGGCATGACATCATCATCGCGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCATC
* * * * *
38905 ATGTAGGAGTCGTGTCACCCCTGATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCGCCC
66 ACGTAGGAGTCGTGTCACCCCTGATAACCAATCGTCCTCATCGCATAGGAAACGTGTTATCACCC
* * ** * *
38970 TTCCTAAAGATGGCATGCCGTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTC
131 CTCATAAAGATGGCATAACGTCCTCATCACGTAGGAACCATGTCATCCCTAGACCAGACCTCCTC
* ***
39035 ATCACGTAGGAGTCATGTCACCCCTAGACAACCTTTCGTCCTCATCACGTAGGAATCGTGTTATC
196 ATCACATAGGAGTCATGTCACCCCTAGACAACCGAACGTCCTCATCACGTAGGAATCGTGTTATC
39100 ATTT
261 ATTT
* * * * * *
39104 CTAAAGATGGCATGTCGTCCTCATCGTGTAGGAACTATGTCATCCCCCGACCAGACCTTCTCATC
1 CTAAAGATGGCATGACATCATCATCGCGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCATC
* * * *
39169 ACGTAGGAG-CTGTGTCACCCCTAGATAATCAATCGTCCTCGTCGTATAGGAAATGTGTTATCAC
66 ACGTAGGAGTC-GTGTCACCCCT-GATAACCAATCGTCCTCATCGCATAGGAAACGTGTTATCAC
* * * * * * *
39233 CCCTCATAAAGATGGCCATAAC-TCTTCATTATGTATGAGCCATGTTATCCAC-AGACCAGATCT
129 CCCTCATAAAGATGG-CATAACGTCCTCATCACGTAGGAACCATGTCATCC-CTAGACCAGACCT
* * * * *
39296 CCTCATCATATAGGAGTCGTGTCACCCTTAGACGACCAGAAC-TCTTCATCACGTA
192 CCTCATCACATAGGAGTCATGTCACCCCTAGACAACC-GAACGTCCTCATCACGTA
39351 TGAGCCGTGT
Statistics
Matches: 203, Mismatches: 39, Indels: 9
0.81 0.16 0.04
Matches are distributed among these distances:
263 1 0.00
264 76 0.37
265 120 0.59
266 6 0.03
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (264 bp):
CTAAAGATGGCATGACATCATCATCGCGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCATC
ACGTAGGAGTCGTGTCACCCCTGATAACCAATCGTCCTCATCGCATAGGAAACGTGTTATCACCC
CTCATAAAGATGGCATAACGTCCTCATCACGTAGGAACCATGTCATCCCTAGACCAGACCTCCTC
ATCACATAGGAGTCATGTCACCCCTAGACAACCGAACGTCCTCATCACGTAGGAATCGTGTTATC
ATTT
Found at i:39530 original size:3 final size:3
Alignment explanation
Indices: 39517--39596 Score: 94
Period size: 3 Copynumber: 26.7 Consensus size: 3
39507 CTACAAAAAA
* *
39517 TAT TA- TAT TAT TATT TAC TAT TAT TA- AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39561 TAT TAT TAT GT-T TAT TAAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT T-AT TAT TAT TAT TAT TAT TA
39597 CAAGTATACA
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.06
3 56 0.84
4 7 0.10
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:40254 original size:22 final size:22
Alignment explanation
Indices: 40210--40254 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40200 AAGGGTAGAT
* *
40210 AAAAAAAGGAGAGAATCGGGAG
1 AAAAAAAAGAGAGAATCGAGAG
40232 AAAAAAACAGAGAGAAT-GAGAG
1 AAAAAAA-AGAGAGAATCGAGAG
40254 A
1 A
40255 GAGTAGAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.60, C:0.04, G:0.31, T:0.04
Consensus pattern (22 bp):
AAAAAAAAGAGAGAATCGAGAG
Found at i:41125 original size:30 final size:29
Alignment explanation
Indices: 41087--41304 Score: 163
Period size: 30 Copynumber: 7.3 Consensus size: 29
41077 TTATTAATAA
*
41087 TTATTATTTTAGTCCTTTTAGTTGTTGTTT
1 TTATTATTTTAGTCCTTTAAGTT-TTGTTT
* * *
41117 TTACTA-TTTAATCCTTTAAGATTTG-TT
1 TTATTATTTTAGTCCTTTAAGTTTTGTTT
* * * *
41144 TTATTATTTTAATCCGTTAAATGTATGTTT
1 TTATTATTTTAGTCCTTTAAGT-TTTGTTT
* * *
41174 TTATTACTTTGGACCTTTAAGTTTCTGTTT
1 TTATTATTTTAGTCCTTTAAGTTT-TGTTT
* * *
41204 ATGTTATTTTAGCCCTTTAAGTTTTTTGTTT
1 TTATTATTTTAGTCCTTTAAG--TTTTGTTT
* *
41235 TTATTATTTTAGTCCTTTAAATTCCTGTTT
1 TTATTATTTTAGTCCTTTAAGTT-TTGTTT
* * * *
41265 ATACTATTTTAGTCCTTTGATTTTATGTTT
1 TTATTATTTTAGTCCTTTAAGTTT-TGTTT
41295 TT-TCTATTTT
1 TTAT-TATTTT
41305 GGTTCTTGAA
Statistics
Matches: 146, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
27 7 0.05
28 15 0.10
29 19 0.13
30 80 0.55
31 22 0.15
32 3 0.02
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.61
Consensus pattern (29 bp):
TTATTATTTTAGTCCTTTAAGTTTTGTTT
Found at i:41143 original size:28 final size:29
Alignment explanation
Indices: 41109--41176 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
41099 TCCTTTTAGT
*
41109 TGTTGTTTTTACTA-TTTAATCCTTTAAGA
1 TGTTGTTTTTACTATTTTAATCCGTTAA-A
*
41138 T-TTG-TTTTATTATTTTAATCCGTTAAA
1 TGTTGTTTTTACTATTTTAATCCGTTAAA
41165 TGTATGTTTTTA
1 TGT-TGTTTTTA
41177 TTACTTTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 9 0.27
28 16 0.48
29 3 0.09
30 5 0.15
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.59
Consensus pattern (29 bp):
TGTTGTTTTTACTATTTTAATCCGTTAAA
Found at i:41252 original size:61 final size:60
Alignment explanation
Indices: 41088--41304 Score: 201
Period size: 61 Copynumber: 3.6 Consensus size: 60
41078 TATTAATAAT
* * * * *
41088 TATTATTTTAGTCCTTTTAGTTGT-TGTTTTTACTA-TTTAATCCTTTAAGATT-TGTTT-
1 TATTATTTTAGTCC-TTTAATTTTATGTTTTTATTATTTTAGTCCTTTAAGTTTCTGTTTA
* * * * * * *
41145 TATTATTTTAATCCGTTAAATGTATGTTTTTATTACTTTGGACCTTTAAGTTTCTGTTTA
1 TATTATTTTAGTCCTTTAATTTTATGTTTTTATTATTTTAGTCCTTTAAGTTTCTGTTTA
* * * * *
41205 TGTTATTTTAGCCCTTTAAGTTTTTTGTTTTTATTATTTTAGTCCTTTAAATTCCTGTTTA
1 TATTATTTTAGTCCTTTAA-TTTTATGTTTTTATTATTTTAGTCCTTTAAGTTTCTGTTTA
* *
41266 TACTATTTTAGTCCTTTGATTTTATGTTTTT-TCTATTTT
1 TATTATTTTAGTCCTTTAATTTTATGTTTTTAT-TATTTT
41305 GGTTCTTGAA
Statistics
Matches: 128, Mismatches: 26, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
56 6 0.05
57 23 0.18
58 13 0.10
59 6 0.05
60 32 0.25
61 48 0.38
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.60
Consensus pattern (60 bp):
TATTATTTTAGTCCTTTAATTTTATGTTTTTATTATTTTAGTCCTTTAAGTTTCTGTTTA
Found at i:42180 original size:2 final size:2
Alignment explanation
Indices: 42175--42303 Score: 80
Period size: 2 Copynumber: 67.5 Consensus size: 2
42165 TTTTTTAGAT
*
42175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
42216 TT TG T- TA TCA GT- TT TA T- TGA -A T- TA TA TA TA TA TA TA TT
1 TA TA TA TA T-A -TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * *
42254 TA CTA T- TT TT TA T- TA TT TA T- TA T- 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
42293 TA TA TA TA TA T
1 TA TA TA TA TA T
42304 TATTTTTACT
Statistics
Matches: 106, Mismatches: 7, Indels: 28
0.75 0.05 0.20
Matches are distributed among these distances:
1 10 0.09
2 92 0.87
3 3 0.03
4 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (2 bp):
TA
Found at i:42244 original size:41 final size:39
Alignment explanation
Indices: 42197--42299 Score: 113
Period size: 41 Copynumber: 2.6 Consensus size: 39
42187 TATATATATA
42197 TATATATATATATATATT-T-TTTGTTATCAGTTTTATTGAAT
1 TATATATATATATATATTATATTTGTTATCA--TTTATT--AT
* *
42238 TATATATATATATAT-TTACTATTTTTTATTATTTATTAT
1 TATATATATATATATATTA-TATTTGTTATCATTTATTAT
42277 TATATATATATATATATATATAT
1 TATATATATATATATAT-TATAT
42300 ATATTATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
39 17 0.31
40 6 0.11
41 23 0.42
42 1 0.02
43 8 0.15
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (39 bp):
TATATATATATATATATTATATTTGTTATCATTTATTAT
Found at i:42267 original size:7 final size:7
Alignment explanation
Indices: 42257--42375 Score: 57
Period size: 7 Copynumber: 16.6 Consensus size: 7
42247 ATATATTTAC
*
42257 TATTTTT
1 TATTATT
42264 TATTATT
1 TATTATT
42271 TATTATT
1 TATTATT
*
42278 ATATATATA
1 -TAT-TATT
*
42287 TATATATA
1 TAT-TATT
42295 TATATATAT
1 TAT-TAT-T
42304 TATT-TT
1 TATTATT
*
42310 TACTTTTT
1 TA-TTATT
42318 TATTATT
1 TATTATT
*
42325 ATTTTATT
1 -TATTATT
42333 TATT-TT
1 TATTATT
*
42339 TTTTATT
1 TATTATT
*
42346 TA-TATA
1 TATTATT
42352 TATT-TT
1 TATTATT
*
42358 TTTTATT
1 TATTATT
* *
42365 TTTTCTT
1 TATTATT
42372 TATT
1 TATT
42376 TTTCTTTATT
Statistics
Matches: 90, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
6 17 0.19
7 38 0.42
8 29 0.32
9 6 0.07
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTATT
Found at i:42279 original size:39 final size:41
Alignment explanation
Indices: 42195--42297 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 41
42185 TATATATATA
*
42195 TATATATATATATATATATTTTTTGTTATCAGTTTTATTGAAT
1 TATATATATATATATATATATTTTGTTATCAG-TTTATT-AAT
* *
42238 TATATATATATATATTTACTATTTT-TTATTA-TTTATT-AT
1 TATATATATATATATATA-TATTTTGTTATCAGTTTATTAAT
42277 TATATATATATATATATATAT
1 TATATATATATATATATATAT
42298 ATATATTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 3 0.05
39 19 0.35
41 6 0.11
43 22 0.40
44 5 0.09
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (41 bp):
TATATATATATATATATATATTTTGTTATCAGTTTATTAAT
Found at i:42361 original size:44 final size:44
Alignment explanation
Indices: 42313--42419 Score: 112
Period size: 43 Copynumber: 2.4 Consensus size: 44
42303 TTATTTTTAC
42313 TTTTTTATTATTAT-TTTATTTATT-TTT-TTTATTTATATATATT
1 TTTTTTATT-TTATCTTTATTT-TTCTTTATTTATTTATATATATT
* * *
42356 TTTTTTATTTTTTCTTTATTTTTCTTTATTTTTTTATATTTATT
1 TTTTTTATTTTATCTTTATTTTTCTTTATTTATTTATATATATT
*
42400 TTACTTACTATTTTATCTTT
1 TT--TT-TTATTTTATCTTT
42420 GCTTTCTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
42 5 0.09
43 19 0.36
44 16 0.30
46 2 0.04
47 11 0.21
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (44 bp):
TTTTTTATTTTATCTTTATTTTTCTTTATTTATTTATATATATT
Found at i:42384 original size:40 final size:40
Alignment explanation
Indices: 42313--42402 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
42303 TTATTTTTAC
42313 TTTTTTATTATTATTTTATTTATTTTTTTTATTTATATATA
1 TTTTTT-TTATTATTTTATTTATTTTTTTTATTTATATATA
* * *
42354 TTTTTTTTATT-TTTTCTTTATTTTTCTTTATTTTTTTATA
1 TTTTTTTTATTATTTTATTTATTTTT-TTTATTTATATATA
*
42394 TTTATTTTA
1 TTTTTTTTA
42403 CTTACTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 13 0.30
40 25 0.57
41 6 0.14
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (40 bp):
TTTTTTTTATTATTTTATTTATTTTTTTTATTTATATATA
Found at i:42384 original size:49 final size:52
Alignment explanation
Indices: 42237--42398 Score: 161
Period size: 51 Copynumber: 3.1 Consensus size: 52
42227 TTTTATTGAA
* * * * *
42237 TTATATATATATATATTTACTATTTTTTATTATTTATTATTATATATATATATATAT
1 TTATATATAT-TATTTTTAC--TTTTTTATTA-TTATT-TTATTTATTTTTTTATAT
*
42294 ATATATATATTATTTTTACTTTTTTATTATTATTTTATTTATTTTTTT-TAT
1 TTATATATATTATTTTTACTTTTTTATTATTATTTTATTTATTTTTTTATAT
* * *
42345 TTATATATATTTTTTTTA-TTTTTT-CT-TTATTTTTCTTTATTTTTTTATAT
1 TTATATATATTATTTTTACTTTTTTATTATTA-TTTTATTTATTTTTTTATAT
42395 TTAT
1 TTAT
42399 TTTACTTACT
Statistics
Matches: 93, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
48 3 0.03
49 16 0.17
50 13 0.14
51 19 0.20
52 10 0.11
53 5 0.05
54 10 0.11
56 8 0.09
57 9 0.10
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (52 bp):
TTATATATATTATTTTTACTTTTTTATTATTATTTTATTTATTTTTTTATAT
Found at i:42413 original size:24 final size:23
Alignment explanation
Indices: 42313--42413 Score: 62
Period size: 24 Copynumber: 4.2 Consensus size: 23
42303 TTATTTTTAC
*
42313 TTTTTTATTATTATTTTA-TTTATT
1 TTTTTTA-T-TTATTTTACTTTATA
** *
42337 TTTTTTATTTATATATATTTTTTTTA
1 TTTTTTATTTAT-T-T-TACTTTATA
* * *
42363 TTTTTTCTTTATTTTTCTTTATT
1 TTTTTTATTTATTTTACTTTATA
42386 TTTTTATATTTATTTTAC-TTACTA
1 TTTTT-TATTTATTTTACTTTA-TA
42410 TTTT
1 TTTT
42414 ATCTTTGCTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
22 4 0.07
23 16 0.26
24 24 0.39
25 2 0.03
26 15 0.25
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTATTTATTTTACTTTATA
Found at i:45535 original size:13 final size:13
Alignment explanation
Indices: 45517--45554 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
45507 CAAAAAGTAA
45517 AAAAAGAGAAAAT
1 AAAAAGAGAAAAT
45530 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
45542 AACAAAG-GAAAAT
1 AA-AAAGAGAAAAT
45555 TAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:46705 original size:32 final size:32
Alignment explanation
Indices: 46627--46720 Score: 118
Period size: 31 Copynumber: 2.9 Consensus size: 32
46617 TGAGGGCATC
* *
46627 TTTGAAGATTCAACATCAAATGTTGGGGTATTT
1 TTTG-AGATTCAACATCAAATATTGGGGCATTT
** *
46660 TTT-TTATTTAACATCAAATATTGGGGCATTT
1 TTTGAGATTCAACATCAAATATTGGGGCATTT
*
46691 TTTGAGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACATCAAATATTGGGGCAT
46721 CTTTGGAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 26 0.51
32 22 0.43
33 3 0.06
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATATTGGGGCATTT
Found at i:46733 original size:32 final size:32
Alignment explanation
Indices: 46620--46733 Score: 115
Period size: 32 Copynumber: 3.6 Consensus size: 32
46610 GGAACAATGA
*
46620 GGGCATC-TTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTTGAA-ATTCAACATCAAATATTG
* *** *
46652 GGGTAT-TTTTTTTATTTAACATCAAATATTG
1 GGGCATCTTTTGAAATTCAACATCAAATATTG
* * *
46683 GGGCATTTTTTGAGATTCAACATCGAATATTG
1 GGGCATCTTTTGAAATTCAACATCAAATATTG
*
46715 GGGCATCTTTGGAAATTCA
1 GGGCATCTTTTGAAATTCA
46734 TGTTACATGC
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
31 21 0.32
32 44 0.68
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (32 bp):
GGGCATCTTTTGAAATTCAACATCAAATATTG
Found at i:47332 original size:106 final size:106
Alignment explanation
Indices: 47209--47425 Score: 312
Period size: 106 Copynumber: 2.0 Consensus size: 106
47199 ATATCGTGCC
* * *
47209 ACTCGAAACAACACAAGTTCAACTCCACAACGAAGGGACGGTTGGTTGTCAATAAA-AATTT-TC
1 ACTCGAAACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGCTGTCAACAAATAATTTAT-
*
47272 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 -CAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
47315 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGCTGTCAACAAATAATTTATT
1 ACTCGAAACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGCTGTCAACAAATAATTTATC
* * * *
47380 AGTTCCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGG
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
47421 ACTCG
1 ACTCG
47426 GAACTATACA
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
106 93 0.94
107 5 0.05
108 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (106 bp):
ACTCGAAACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGCTGTCAACAAATAATTTATC
AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:47770 original size:87 final size:87
Alignment explanation
Indices: 47679--47860 Score: 301
Period size: 87 Copynumber: 2.1 Consensus size: 87
47669 TGAGACAGTT
*
47679 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTT
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTT
* *
47744 TCTCTTGAAACGAAATTTTGTC
66 TCCCTTGAAACAAAATTTTGTC
* * *
47766 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTT
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTT
47831 TCCCTTGAAACAAAATTTTGTC
66 TCCCTTGAAACAAAATTTTGTC
*
47853 TCCCTTGA
1 TCTCTTGA
47861 GACAGTTTCT
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (87 bp):
TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTT
TCCCTTGAAACAAAATTTTGTC
Found at i:47868 original size:37 final size:37
Alignment explanation
Indices: 47793--47981 Score: 132
Period size: 37 Copynumber: 5.4 Consensus size: 37
47783 ATTGAAAACA
* * * * *
47793 TTTCCCTTGAAA-TAAATTTTATCTCGCTTGGGGTAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
47829 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
* * * *
47866 TTTCTCTTGAAACATAAA---------CATTGA-AAACA
1 TTTCCCTTGAAACA-AAATTTTGTCTCCCTTGAGATA-G
** ** *
47895 TTTCTTTTGAAA-TTAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
47931 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
47968 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
47982 TAAACCTTGA
Statistics
Matches: 116, Mismatches: 23, Indels: 27
0.70 0.14 0.16
Matches are distributed among these distances:
27 2 0.02
28 2 0.02
29 16 0.14
36 26 0.22
37 67 0.58
38 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
Found at i:47879 original size:102 final size:102
Alignment explanation
Indices: 47766--48008 Score: 396
Period size: 102 Copynumber: 2.4 Consensus size: 102
47756 AAATTTTGTC
* *
47766 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTT
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTT
47831 TCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTT
66 TCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTT
** * * *
47868 TCTCTTGAAACATAAACATTGAAAACATTTCTTTTGAAATTAATTTTGTCTCTCTTGAGATAGTT
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTT
*
47933 TCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAGTT
66 TCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTT
* *
47970 TCTCTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
48009 CACAAAATAT
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 129 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
TCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTT
TCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTT
Found at i:48096 original size:37 final size:37
Alignment explanation
Indices: 48046--48148 Score: 181
Period size: 36 Copynumber: 2.8 Consensus size: 37
48036 AAAACGAGTT
48046 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
* *
48083 TTGAGACAATTTCCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
48119 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
48149 TGAATATCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 34 0.56
37 27 0.44
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:48214 original size:102 final size:102
Alignment explanation
Indices: 48059--48245 Score: 261
Period size: 102 Copynumber: 1.8 Consensus size: 102
48049 AGACAGTTTC
*
48059 CCTTGAAACAAAATCTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
1 CCTTGAAACAAAATCTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
48124 ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
66 ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * * * * *
48161 CCTTGAAAC-AAATTTTGTCTCCCTTGAGATAGTTT-CTTTTAGAACTAAGTTTTGTCTCTCTTG
1 CCTTGAAACAAAATCTTGTCTCCCTTGAGACAATTTCCCTTGA-AAC-AAATTTTGTCTCTCTTG
**
48224 AGACAGTTTCTTTTGAAACAAA
64 AGACAGTTTCCCTTGAAACAAA
48246 TTTTGTCCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
100 4 0.05
101 25 0.34
102 45 0.61
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (102 bp):
CCTTGAAACAAAATCTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:48258 original size:36 final size:36
Alignment explanation
Indices: 48158--48279 Score: 158
Period size: 36 Copynumber: 3.4 Consensus size: 36
48148 TTGAATATCT
* *
48158 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
48193 TTTCT-TTTAGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGA-AAC-AAATTTTGTCTCTCTTGAGACAG
* *
48230 TTTCTTTTGAAACAAATTTTGTCCCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
48266 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
48280 CAAAAAAACC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
35 7 0.09
36 37 0.49
37 28 0.37
38 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:49470 original size:21 final size:23
Alignment explanation
Indices: 49418--49472 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
49408 GTTTTATTAT
49418 TTTTCTTTTCTTTTTTTCATGTAA
1 TTTTCTTTT-TTTTTTTCATGTAA
* *
49442 TATT-TTTTTTTTTTT-ATG-CA
1 TTTTCTTTTTTTTTTTCATGTAA
49462 TTTTCTTTTTT
1 TTTTCTTTTTT
49473 AGTTTAGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
22 7 0.26
23 4 0.15
24 3 0.11
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTCTTTTTTTTTTTCATGTAA
Found at i:49503 original size:8 final size:9
Alignment explanation
Indices: 49484--49666 Score: 63
Period size: 9 Copynumber: 19.7 Consensus size: 9
49474 GTTTAGTATA
49484 TATTTTTAT
1 TATTTTTAT
49493 TATTTTTTTAT
1 TA--TTTTTAT
49504 TATCAGTTTTAT
1 TAT---TTTTAT
*
49516 TGATTTATAT
1 T-ATTTTTAT
* *
49526 ATATATTTAC
1 -TATTTTTAT
49536 TATTTTTTAT
1 TA-TTTTTAT
*
49546 TATTTAT-T
1 TATTTTTAT
*
49554 TATTATATAT
1 TATT-TTTAT
* *
49564 ATATATATAT
1 -TATTTTTAT
*
49574 T-TTTTTAC
1 TATTTTTAT
49582 T-TTTTTAT
1 TATTTTTAT
*
49590 TATTATT-T
1 TATTTTTAT
*
49598 TATTTAT-T
1 TATTTTTAT
49606 TATTTGTT-T
1 TATTT-TTAT
*
49615 TATTTATAT
1 TATTTTTAT
* *
49624 TTTTTTTCT
1 TATTTTTAT
* *
49633 TCTTTTTCTT
1 TATTTTT-AT
*
49643 TATTTTTTT
1 TATTTTTAT
*
49652 TATTTTTTT
1 TATTTTTAT
49661 TATTTT
1 TATTTT
49667 ACTTACTATT
Statistics
Matches: 136, Mismatches: 23, Indels: 30
0.72 0.12 0.16
Matches are distributed among these distances:
8 30 0.22
9 54 0.40
10 30 0.22
11 13 0.10
12 7 0.05
13 2 0.01
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (9 bp):
TATTTTTAT
Found at i:49554 original size:4 final size:4
Alignment explanation
Indices: 49511--49621 Score: 63
Period size: 4 Copynumber: 28.2 Consensus size: 4
49501 TATTATCAGT
* * * *
49511 TTTA TTGA TTTA TATA TATA TTTA -CTA TTT- TTTA -TTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
49556 TTATA TATA TATA TATA TTTT TTTA CTTT- TTTA -TTA -TTA TTTTA TTTA
1 TT-TA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA -TTTA TTTA
*
49604 TTTA TTTGT TTTA TTTA T
1 TTTA TTT-A TTTA TTTA T
49622 ATTTTTTTTC
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
3 17 0.20
4 57 0.66
5 12 0.14
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:49560 original size:36 final size:37
Alignment explanation
Indices: 49511--49621 Score: 104
Period size: 36 Copynumber: 3.0 Consensus size: 37
49501 TATTATCAGT
* *
49511 TTTATTGATT-TATATATATATTTACTATTTTTTA-TTA
1 TTTATTTATTATATATATATATATA-T-TTTTTTACTTA
*
49548 TTTATTTATTATATATATATATATATTTTTTTACTTT
1 TTTATTTATTATATATATATATATATTTTTTTACTTA
* * * *
49585 TTTA-TTATTAT-TTTATTTATTTATTTGTTTTATTTA
1 TTTATTTATTATATATATATATATATTT-TTTTACTTA
49621 T
1 T
49622 ATTTTTTTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
35 12 0.19
36 22 0.35
37 16 0.25
38 13 0.21
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (37 bp):
TTTATTTATTATATATATATATATATTTTTTTACTTA
Found at i:49598 original size:19 final size:19
Alignment explanation
Indices: 49492--49621 Score: 70
Period size: 20 Copynumber: 6.4 Consensus size: 19
49482 TATATTTTTA
* *
49492 TTATTTTTTTATTATCAGTT
1 TTATTTATTTATTATTA-TT
*
49512 TTATTGATTTATATATATATT
1 TTATTTATTTAT-TAT-TATT
49533 TACTATTT-TTTATTATTTATTT
1 T--TATTTATTTATTA-TTA-TT
* *
49555 ATTATATATATATATATATTTTT
1 -TTAT-T-TATTTAT-TATTATT
49578 TTACTTT-TTTATTATTATT
1 TTA-TTTATTTATTATTATT
*
49597 TTATTTATTTA-T-TTGTT
1 TTATTTATTTATTATTATT
49614 TTATTTAT
1 TTATTTAT
49622 ATTTTTTTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 29
0.70 0.07 0.23
Matches are distributed among these distances:
17 12 0.14
18 4 0.05
19 13 0.15
20 14 0.16
21 14 0.16
22 14 0.16
23 9 0.10
24 6 0.07
25 2 0.02
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTATTTATTTATTATTATT
Found at i:49623 original size:52 final size:50
Alignment explanation
Indices: 49545--49656 Score: 122
Period size: 52 Copynumber: 2.2 Consensus size: 50
49535 CTATTTTTTA
49545 TTATTTATTTATTATATATATATATATATTTTTTTACTT-TTTTAT-TATTATT
1 TTATTTATTTATTATATATATATATAT-TTTTTTT-CTTCTTTT-TCT-TTATT
* * *
49597 TTATTTATTTATT-TGTTTTATTTATATTTTTTTTCTTCTTTTTCTTTATT
1 TTATTTATTTATTAT-ATATATATATATTTTTTTTCTTCTTTTTCTTTATT
*
49647 TTTTTTATTT
1 TTATTTATTT
49657 TTTTTATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
50 18 0.34
51 13 0.25
52 22 0.42
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.75
Consensus pattern (50 bp):
TTATTTATTTATTATATATATATATATTTTTTTTCTTCTTTTTCTTTATT
Found at i:58515 original size:3 final size:3
Alignment explanation
Indices: 58507--58531 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
58497 TAACGGCATC
58507 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
58532 CAGTAGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.