Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000973.1 Hibiscus syriacus cultivar Beakdansim tig00001947_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: 80918
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:2466 original size:6 final size:6
Alignment explanation
Indices: 2455--2500 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
2445 AGACGTATTA
* *
2455 CACGAC CACGAC CACGAC CACGAC C-CGAC CACGAC GACGAC GACGA
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
2501 GACGAGACGG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.33, C:0.46, G:0.22, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:2483 original size:23 final size:23
Alignment explanation
Indices: 2457--2500 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2447 ACGTATTACA
2457 CGACCACGACCACGACCACGACC
1 CGACCACGACCACGACCACGACC
* *
2480 CGACCACGACGACGACGACGA
1 CGACCACGACCACGACCACGA
2501 GACGAGACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.45, G:0.23, T:0.00
Consensus pattern (23 bp):
CGACCACGACCACGACCACGACC
Found at i:3015 original size:21 final size:21
Alignment explanation
Indices: 2976--3020 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2966 GTTCGTCTCA
2976 GGTCGGGTCGGGTCGGGTCGT
1 GGTCGGGTCGGGTCGGGTCGT
*
2997 GGTCGTGGTCGTGTC-GGTCGT
1 GGTCG-GGTCGGGTCGGGTCGT
3018 GGT
1 GGT
3021 AATACGTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (21 bp):
GGTCGGGTCGGGTCGGGTCGT
Found at i:3144 original size:22 final size:22
Alignment explanation
Indices: 3116--3168 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
3106 AATTTGGAAA
3116 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
3138 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
3160 ATCGCAACG
1 ATCGCAACG
3169 CGAAATGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:6174 original size:20 final size:20
Alignment explanation
Indices: 6148--6309 Score: 108
Period size: 20 Copynumber: 8.0 Consensus size: 20
6138 CAAATTCGCG
6148 TTGCATTTCGCGTTGCGATT
1 TTGCATTTCGCGTTGCGATT
* *
6168 TTTCATTTCGCGTTGCGATAG
1 TTGCATTTCGCGTTGCGAT-T
* **
6189 TTGAAAATCGCGTTGCGATT
1 TTGCATTTCGCGTTGCGATT
* * * *
6209 TTCCATTTCGCGTTACAATAG
1 TTGCATTTCGCGTTGCGAT-T
* ** ** *
6230 TTGAAAATAACGTTGCGATAG
1 TTGCATTTCGCGTTGCGAT-T
* ** *
6251 TTGAAAGTCGCATTGCGATT
1 TTGCATTTCGCGTTGCGATT
*
6271 TTTCATTTCGCGTTGCGATT
1 TTGCATTTCGCGTTGCGATT
*
6291 TTCCATTTCGCGTTGCGAT
1 TTGCATTTCGCGTTGCGAT
6310 AGTCTACAGT
Statistics
Matches: 107, Mismatches: 33, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
20 64 0.60
21 43 0.40
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCATTTCGCGTTGCGATT
Found at i:6201 original size:21 final size:21
Alignment explanation
Indices: 6175--6269 Score: 84
Period size: 21 Copynumber: 4.6 Consensus size: 21
6165 ATTTTTCATT
6175 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
6196 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* *
6216 TCGCGTTACAATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
** *
6237 TAACGTTGCGATAGTTGAAAG
1 TCGCGTTGCGATAGTTGAAAA
*
6258 TCGCATTGCGAT
1 TCGCGTTGCGAT
6270 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 20, Indels: 2
0.71 0.27 0.03
Matches are distributed among these distances:
20 13 0.25
21 40 0.75
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:6202 original size:41 final size:41
Alignment explanation
Indices: 6155--6312 Score: 156
Period size: 41 Copynumber: 3.9 Consensus size: 41
6145 GCGTTGCATT
*
6155 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* *
6196 TCGCGTTGCGATTTTCCATTTCGCGTTACAATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
** * ** ** * * ** **
6237 TAACGTTGCGATAGTTGAAAGTCGCATTGCGAT-TTTTCATT
1 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTGAAAA
6278 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
6313 CTACAGTTGT
Statistics
Matches: 88, Mismatches: 27, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
40 14 0.16
41 62 0.70
42 12 0.14
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:6329 original size:22 final size:22
Alignment explanation
Indices: 6301--6353 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
6291 TTCCATTTCG
6301 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
6323 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
6345 CATTGCGAT
1 CGTTGCGAT
6354 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:6331 original size:62 final size:61
Alignment explanation
Indices: 6151--6312 Score: 198
Period size: 62 Copynumber: 2.6 Consensus size: 61
6141 ATTCGCGTTG
* *
6151 CATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAGTCGCGTTGCGATTTTC
* * * ** ** ** * *
6212 CATTTCGCGTTACAATAGTTGAAAATAACGTTGCGATAGTTGAAAGTCGCATTGCGATTTTT
1 CATTTCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTGAAAGTCGCGTTGCGATTTTC
6274 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
6313 CTACAGTTGT
Statistics
Matches: 79, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
61 30 0.38
62 49 0.62
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (61 bp):
CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAGTCGCGTTGCGATTTTC
Found at i:7107 original size:22 final size:22
Alignment explanation
Indices: 7079--7131 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
7069 AATTTGGAAA
7079 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
7101 ATCGCAACAACAACTGTAGATT
1 ATCGCAACGACAACTGTAGACT
7123 ATCGCAACG
1 ATCGCAACG
7132 CGAAATGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:11541 original size:31 final size:31
Alignment explanation
Indices: 11503--11585 Score: 148
Period size: 31 Copynumber: 2.7 Consensus size: 31
11493 GTCCATAGAT
* *
11503 TCCCGAAGAACCTAGGTAATCAGTCCATATG
1 TCCCGAAGAACATAGGTAAACAGTCCATATG
11534 TCCCGAAGAACATAGGTAAACAGTCCATATG
1 TCCCGAAGAACATAGGTAAACAGTCCATATG
11565 TCCCGAAGAACATAGGTAAAC
1 TCCCGAAGAACATAGGTAAAC
11586 CCTCGACCCT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
TCCCGAAGAACATAGGTAAACAGTCCATATG
Found at i:13761 original size:25 final size:25
Alignment explanation
Indices: 13733--13801 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
13723 TATATATATA
13733 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
13758 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
* *
13783 TCCTGAATGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
13802 CCCTCTACTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:15493 original size:21 final size:21
Alignment explanation
Indices: 15469--15513 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
15459 TTTTGTTCGT
* *
15469 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
15490 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
15511 TTG
1 TTG
15514 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:18805 original size:23 final size:23
Alignment explanation
Indices: 18779--18823 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
18769 CACCACAGCT
*
18779 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
18802 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
18824 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:18966 original size:25 final size:26
Alignment explanation
Indices: 18931--18981 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
18921 CAAAGAATAT
18931 ATATATATCCCGAAGGACCGCGTAGA
1 ATATATATCCCGAAGGACCGCGTAGA
18957 ATAT-TATCCCGAAGGACCGCGTAGA
1 ATATATATCCCGAAGGACCGCGTAGA
18982 CCCTCTACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (26 bp):
ATATATATCCCGAAGGACCGCGTAGA
Found at i:24684 original size:31 final size:31
Alignment explanation
Indices: 24649--24726 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
24639 ATAGATTCCA
* *
24649 AAGAACCTAGGTAATCA-TTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTT-CATATGTCCCG
24680 AAGAACATAGGTAAACAGTTCATATGTCCCG
1 AAGAACATAGGTAAACAGTTCATATGTCCCG
24711 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
24727 CCTCGACCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 42 0.95
32 2 0.05
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.22
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTTCATATGTCCCG
Found at i:28838 original size:26 final size:26
Alignment explanation
Indices: 28809--28861 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28799 ATGATACTAT
28809 AAATATAGTAAACTAAGTTAGAAAAG
1 AAATATAGTAAACTAAGTTAGAAAAG
28835 AAATATAGTAAACTAAGTTAGAAAAG
1 AAATATAGTAAACTAAGTTAGAAAAG
28861 A
1 A
28862 TCTGTTCTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.04, G:0.15, T:0.23
Consensus pattern (26 bp):
AAATATAGTAAACTAAGTTAGAAAAG
Found at i:29102 original size:6 final size:6
Alignment explanation
Indices: 29091--29131 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
29081 TTTATACCTT
29091 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
29132 GTAGCAAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CTCTCC
Found at i:37334 original size:2 final size:2
Alignment explanation
Indices: 37327--37354 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37317 ACCATATAAC
37327 AT 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 AT
37355 CATGTCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37693 original size:29 final size:30
Alignment explanation
Indices: 37651--37724 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
37641 GTCCCGAAGG
*
37651 AACTATCCAGAGGTCACAAAG-ACCCCGGT
1 AACTATCCAGAGGTCACAAAGAACCCCGGC
* *
37680 AACTATCCAGAGGTCATAAAGAACCTCGGC
1 AACTATCCAGAGGTCACAAAGAACCCCGGC
* *
37710 AACTGTCCATAGGTC
1 AACTATCCAGAGGTC
37725 CCGATGAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (30 bp):
AACTATCCAGAGGTCACAAAGAACCCCGGC
Found at i:37754 original size:31 final size:31
Alignment explanation
Indices: 37710--37805 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
37700 GAACCTCGGC
*
37710 AACTGTCCATAGGTCCCGATGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
* *
37741 AATTGTTCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
* * *
37772 AACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTCCCGAAGA-ACCTAGGTA
37803 AAC
1 AAC
37806 CCTCGACTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 1 0.02
31 55 0.98
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:38732 original size:20 final size:22
Alignment explanation
Indices: 38707--38764 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
38697 TTCCCCTTGA
38707 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
38727 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
38750 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
38765 CTACCCATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:38828 original size:64 final size:63
Alignment explanation
Indices: 38752--38892 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
38742 TCTTTAACAT
* *
38752 GTGCATCGATGCACTACC-CATACATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATACATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * * *
38815 GATGCATCGATGCACTCCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATACATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
38879 GTGCATCGATGCAC
1 GTGCATCGATGCAC
38893 ATTCAATGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 21 0.32
64 45 0.68
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATACATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:44826 original size:126 final size:127
Alignment explanation
Indices: 44625--44932 Score: 519
Period size: 126 Copynumber: 2.4 Consensus size: 127
44615 AAAATGATGG
* * * *
44625 GAAATGATTCCCTAAACACAACTAGGGAGTTACTTTCTTCGTTAATTAAAAATAAACAAATCGTT
1 GAAATAATTTCCTTAACACAACTAGGGAGTTACTTTCTTCGTTAATTAAAAATAAACAAATCATT
* *
44690 TCATATTTTTCTTAATTTTTGGAAATACAGAAAATGCTAACATTATTTCAATTAGAACATAA
66 TCATATTTTTCTTAATTTTTGAAAATACAAAAAATGCTAACATTATTTCAATTAGAACATAA
*
44752 GAAATAATTTCCTTAACACAACTA-GGAGTTACTTTCTTCGTTAATTAAAAATAAACAAATTATT
1 GAAATAATTTCCTTAACACAACTAGGGAGTTACTTTCTTCGTTAATTAAAAATAAACAAATCATT
*
44816 TCATATTTTTCTTAATTTTTGAAAATATAAAAAATGCTAACATTATTTCAATTAGAACATAA
66 TCATATTTTTCTTAATTTTTGAAAATACAAAAAATGCTAACATTATTTCAATTAGAACATAA
* *
44878 GAAATAATTTCCTTAACACAACTAGGGAGTTAATTTCTTCATTAATTAAAAATAA
1 GAAATAATTTCCTTAACACAACTAGGGAGTTACTTTCTTCGTTAATTAAAAATAA
44933 TAATAGACAT
Statistics
Matches: 170, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
126 121 0.71
127 49 0.29
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (127 bp):
GAAATAATTTCCTTAACACAACTAGGGAGTTACTTTCTTCGTTAATTAAAAATAAACAAATCATT
TCATATTTTTCTTAATTTTTGAAAATACAAAAAATGCTAACATTATTTCAATTAGAACATAA
Found at i:45058 original size:3 final size:3
Alignment explanation
Indices: 45052--45076 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45042 TTTAATTAGA
45052 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
45077 TTTTTTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:45800 original size:21 final size:20
Alignment explanation
Indices: 45761--45803 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
45751 CAATTAATGA
45761 ATTTTATTTAAATATAAATT
1 ATTTTATTTAAATATAAATT
*
45781 ATTTTATCTTAAA-ATAAAAT
1 ATTTTAT-TTAAATATAAATT
45801 ATT
1 ATT
45804 GAAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTATTTAAATATAAATT
Found at i:47232 original size:15 final size:16
Alignment explanation
Indices: 47207--47237 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
47197 TTAAAAATAA
47207 TTATAATAATAATTTT
1 TTATAATAATAATTTT
47223 TTAT-ATAATAATTTT
1 TTATAATAATAATTTT
47238 CAATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATAATAATAATTTT
Found at i:48746 original size:27 final size:28
Alignment explanation
Indices: 48696--48755 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
48686 AAATCTTTTT
* * * *
48696 TATTTTTTAATTGTTAATAGAATAAATG
1 TATTTTTGAATGGTTAATAAAATAAATA
48724 TATTTTTGAATGGTTAA-AAAATAAATA
1 TATTTTTGAATGGTTAATAAAATAAATA
48751 TATTT
1 TATTT
48756 CATATATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (28 bp):
TATTTTTGAATGGTTAATAAAATAAATA
Found at i:51316 original size:35 final size:35
Alignment explanation
Indices: 51204--51381 Score: 100
Period size: 40 Copynumber: 4.9 Consensus size: 35
51194 AAATGGTTTC
* * *
51204 TGAAAATATATATATAATATAGTTTTTTTAAAAACGTTTT
1 TGAAAAT-TATATACAATATA--TATTTT-AAAAC-ATTT
51244 TGAAAACTTATATACAATATATAAGTTTTAAAACATTT
1 TGAAAA-TTATATACAATATAT-A-TTTTAAAACATTT
*
51282 TGAAAATTATATA-ACATATAT-TTTTGAAATCATTT
1 TGAAAATTATATACA-ATATATATTTT-AAAACATTT
* *
51317 TG-AAA--ATAT--AATGTATAGTTTAAAAAAACATTTT
1 TGAAAATTATATACAATATATA-TTT--TAAAACA-TTT
* *
51351 TGAAAATTTTATATAATATATAGTTTTAAAA
1 TGAAAATTATATACAATATATA-TTTTAAAA
51382 ATATTTTGGA
Statistics
Matches: 113, Mismatches: 10, Indels: 33
0.72 0.06 0.21
Matches are distributed among these distances:
30 5 0.04
31 1 0.01
32 7 0.06
33 5 0.04
34 12 0.11
35 13 0.12
36 1 0.01
37 20 0.18
38 10 0.09
39 16 0.14
40 22 0.19
41 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (35 bp):
TGAAAATTATATACAATATATATTTTAAAACATTT
Found at i:51354 original size:69 final size:68
Alignment explanation
Indices: 51273--51482 Score: 187
Period size: 71 Copynumber: 3.0 Consensus size: 68
51263 TATAAGTTTT
*
51273 AAAACA-TTTTGAAAATTATATAACATATATTTTTGAAATCATTTTGAAAATATAATGTATAGTT
1 AAAACATTTTTGAAAATTATATAATATATATTTTTGAAATCATTTTGAAAATATAAT-TATAGTT
51337 TAAA
65 TAAA
** *
51341 AAAACATTTTTGAAAATTTTATATAATATATAGTTTTAAAAAT-ATTTTGGAAAACTCAT-ATAA
1 AAAACATTTTTGAAAA--TTATATAATATATA-TTTTTGAAATCATTTT-GAAAA-T-ATAATTA
**
51404 TA-TTTTTA
60 TAGTTTAAA
** * ** * * *
51412 AAATTATTTTTGAAAACTATATGGTATATAGTTTTGAAAACATTTT-TAAATATAATATATAGTT
1 AAAACATTTTTGAAAATTATATAATATATATTTTTGAAATCATTTTGAAAATATAAT-TATAGTT
51476 TAAA
65 TAAA
51480 AAA
1 AAA
51483 TATTTTTTGA
Statistics
Matches: 112, Mismatches: 19, Indels: 22
0.73 0.12 0.14
Matches are distributed among these distances:
65 2 0.02
66 3 0.03
67 6 0.05
68 19 0.17
69 25 0.22
71 36 0.32
72 16 0.14
73 3 0.03
74 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (68 bp):
AAAACATTTTTGAAAATTATATAATATATATTTTTGAAATCATTTTGAAAATATAATTATAGTTT
AAA
Found at i:51420 original size:33 final size:31
Alignment explanation
Indices: 51366--51433 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 31
51356 ATTTTATATA
51366 ATATATAGTTTTAAAAATATTTTGGAAAACT
1 ATATATAGTTTTAAAAATATTTTGGAAAACT
* * *
51397 CATATAATATTTTTAAAATTATTTTTGAAAACT
1 -ATAT-ATAGTTTTAAAAATATTTTGGAAAACT
51430 ATAT
1 ATAT
51434 GGTATATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 8 0.25
33 24 0.75
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (31 bp):
ATATATAGTTTTAAAAATATTTTGGAAAACT
Found at i:51521 original size:17 final size:16
Alignment explanation
Indices: 51499--51530 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
51489 TTGAGATATA
51499 TATATTATTATATAGTC
1 TATATTATTAT-TAGTC
51516 TATATTATTATTAGT
1 TATATTATTATTAGT
51531 ATTTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.56
Consensus pattern (16 bp):
TATATTATTATTAGTC
Found at i:51568 original size:18 final size:18
Alignment explanation
Indices: 51547--51585 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
51537 ATTATTTCTT
*
51547 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
51565 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
51583 TTC
1 TTC
51586 TGTTTTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:56598 original size:106 final size:106
Alignment explanation
Indices: 56413--57665 Score: 2220
Period size: 106 Copynumber: 11.8 Consensus size: 106
56403 TACAGCCTTT
*
56413 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
56478 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
56519 AGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
56584 CGAAGGGACCGCTGGTTCTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
56625 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
56690 CGAAGGGACCGCTGGTTTTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
56731 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
56796 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
56837 AGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
56902 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
* *
56943 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
57008 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
57049 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
57114 AGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
57155 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
57220 CGAAGGGACCGTTGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
*
57261 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
57326 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTT
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
57367 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
57432 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
* * *
57473 AGAGCCAATTTCAACTTCACAGCGAAGGGTATTGGACTCCAGACAACGCATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
57538 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
* * * * *
57579 AGAGCCAATTTCAACTTCACAGCGAAGGATATGGGACTCCAGACAATGCATGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
57644 CGAAGGGA-CGACTGATTGTCAA
66 CGAAGGGACCG-CTGGTTGTCAA
57666 CAAACAATTT
Statistics
Matches: 1104, Mismatches: 42, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
105 2 0.00
106 1102 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
Found at i:58138 original size:84 final size:82
Alignment explanation
Indices: 57907--58257 Score: 287
Period size: 84 Copynumber: 4.2 Consensus size: 82
57897 TCTGCCAACA
* * * * *
57907 AAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGTATAGCTTAGGTCG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTA-ATCT
* *
57971 AGAAGGG--CTATCTG-CC
64 AGAAGGGTTATATGTGACC
** * * * * * * *
57987 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAA-TCT
58052 AGAAGGGTTATATGTGACC
64 AGAAGGGTTATATGTGACC
* * *
58071 AAAAGATCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTGAATCT
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTT-AATCT
* * **
58136 AGAAGGGTTGTCTGCCAACC
64 AGAAGGGTTATATG-TGACC
* * * * *
58156 AAAGACCTTCGAGTTCGACTACGCTTAACTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA-TCTA
** * * * *
58221 GAAAAGCTATCTGTCAAC
65 GAAGGGTTATATGTGACC
58239 AAAGACCTTTCGAGTTCGA
1 AAAGACC-TTCGAGTTCGA
58258 GTTCGTTCAG
Statistics
Matches: 213, Mismatches: 47, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
80 24 0.11
81 30 0.14
82 1 0.00
83 16 0.08
84 113 0.53
85 29 0.14
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (82 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAATCTAG
AAGGGTTATATGTGACC
Found at i:58815 original size:35 final size:35
Alignment explanation
Indices: 58740--58880 Score: 98
Period size: 37 Copynumber: 3.9 Consensus size: 35
58730 TTAAAAACGT
58740 TTTTGAAAACTTATATACAATATATAAGTTTTAAAACA
1 TTTTGAAAA-TTATATACAATATAT-A-TTTTAAAACA
*
58778 TTTTGAAAATTATATA-ACATATAT-TTTTGAAATCA
1 TTTTGAAAATTATATACA-ATATATATTTT-AAAACA
* *
58813 TTTTG-AAA--ATAT--AATGTATAGTTTAAAAAAACA
1 TTTTGAAAATTATATACAATATATA-TTT--TAAAACA
* *
58846 TTTTTGAAAATTTTATATAATATATAGTTTTAAAA
1 -TTTTGAAAATTATATACAATATATA-TTTTAAAA
58881 ATATTTTGGA
Statistics
Matches: 84, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
30 5 0.06
31 1 0.01
32 7 0.08
33 5 0.06
34 12 0.14
35 13 0.15
36 1 0.01
37 20 0.24
38 9 0.11
39 11 0.13
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (35 bp):
TTTTGAAAATTATATACAATATATATTTTAAAACA
Found at i:58853 original size:69 final size:68
Alignment explanation
Indices: 58772--58981 Score: 196
Period size: 71 Copynumber: 3.0 Consensus size: 68
58762 TATAAGTTTT
*
58772 AAAACA-TTTTGAAAATTATATAACATATATTTTTGAAATCATTTTGAAAATATAATGTATAGTT
1 AAAACATTTTTGAAAATTATATAATATATATTTTTGAAATCATTTTGAAAATATAAT-TATAGTT
58836 TAAA
65 TAAA
** *
58840 AAAACATTTTTGAAAATTTTATATAATATATAGTTTTAAAAAT-ATTTTGGAAAACTCAT-ATAA
1 AAAACATTTTTGAAAA--TTATATAATATATA-TTTTTGAAATCATTTT-GAAAA-T-ATAATTA
**
58903 TA-TTTTTA
60 TAGTTTAAA
* * ** * * *
58911 AAATCATTTTTGAAAACTATATGGTATATAGTTTTGAAAACATTTT-TAAATATAATATATAGTT
1 AAAACATTTTTGAAAATTATATAATATATATTTTTGAAATCATTTTGAAAATATAAT-TATAGTT
58975 TAAA
65 TAAA
58979 AAA
1 AAA
58982 TATTTTTTGA
Statistics
Matches: 113, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
65 2 0.02
66 3 0.03
67 6 0.05
68 19 0.17
69 25 0.22
71 37 0.33
72 16 0.14
73 3 0.03
74 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (68 bp):
AAAACATTTTTGAAAATTATATAATATATATTTTTGAAATCATTTTGAAAATATAATTATAGTTT
AAA
Found at i:58920 original size:33 final size:31
Alignment explanation
Indices: 58865--58932 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 31
58855 ATTTTATATA
58865 ATATATAGTTTTAAAAATATTTTGGAAAACT
1 ATATATAGTTTTAAAAATATTTTGGAAAACT
* *
58896 CATATAATA-TTTTTAAAATCATTTTTGAAAACT
1 -ATAT-ATAGTTTTAAAAAT-ATTTTGGAAAACT
58929 ATAT
1 ATAT
58933 GGTATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATATAGTTTTAAAAATATTTTGGAAAACT
Found at i:59002 original size:139 final size:139
Alignment explanation
Indices: 58662--59012 Score: 334
Period size: 139 Copynumber: 2.4 Consensus size: 139
58652 TTGAAAGTGT
* *
58662 TTTTGAAAAATATAACATATAGTTTACAAAAAAATGGTTTCTGAATATATATAT-ATAATATAGT
1 TTTTG-AAAATATAATATATAGTTT--AAAAAAAT--TTTTTGAATATATATATAAT-ATATAG-
* * * *
58726 TTTTTTAAAAACGTTTTTGAAAACTTATATACAATATATAAGTTTTAAAACATTTTGAAAATTAT
59 --TTTTAAAAACATTTTGGAAAACTCATAT--AATATAT-A-TTTTAAAACATTTTGAAAACTAT
* *
58791 ATAACATATATTTTTGAAATCA
118 ATAACATATAGTTTTGAAAACA
* * * *
58813 TTTTGAAAATATAATGTATAGTTTAAAAAAACATTTTTGAAAATTTTATATAATATATAGTTTTA
1 TTTTGAAAATATAATATATAGTTTAAAAAAA-TTTTTTGAATA-TATATATAATATATAGTTTTA
* ***
58878 AAAATATTTTGGAAAACTCATAT-A-ATAT-TTTTAAAATCATTTTTGAAAACTATATGGTATAT
64 AAAACATTTTGGAAAACTCATATAATATATATTTTAAAA-CA-TTTTGAAAACTATATAACATAT
58940 AGTTTTGAAAACA
127 AGTTTTGAAAACA
* *
58953 TTTT-TAAATATAATATATAGTTTAAAAAATATTTTTTGAGATATATATATATTATATAGT
1 TTTTGAAAATATAATATATAGTTTAAAAAA-ATTTTTTGA-ATATATATATAATATATAGT
59013 CTATATTATT
Statistics
Matches: 171, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
138 8 0.05
139 47 0.27
140 36 0.21
141 4 0.02
142 1 0.01
145 24 0.14
147 8 0.05
148 19 0.11
149 2 0.01
150 17 0.10
151 5 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (139 bp):
TTTTGAAAATATAATATATAGTTTAAAAAAATTTTTTGAATATATATATAATATATAGTTTTAAA
AACATTTTGGAAAACTCATATAATATATATTTTAAAACATTTTGAAAACTATATAACATATAGTT
TTGAAAACA
Found at i:59066 original size:18 final size:18
Alignment explanation
Indices: 59045--59083 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
59035 ATTATTTCTT
*
59045 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
59063 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
59081 TTC
1 TTC
59084 TGTTTTATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:66856 original size:22 final size:22
Alignment explanation
Indices: 66831--66878 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
66821 TAAAGGCATG
66831 CATTAGTTTGTCCTTCCATCTT
1 CATTAGTTTGTCCTTCCATCTT
66853 CATTAGTTTGTCCTTCCATCTT
1 CATTAGTTTGTCCTTCCATCTT
66875 CATT
1 CATT
66879 CCATATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.08, T:0.50
Consensus pattern (22 bp):
CATTAGTTTGTCCTTCCATCTT
Found at i:75690 original size:22 final size:22
Alignment explanation
Indices: 75665--76114 Score: 506
Period size: 22 Copynumber: 20.6 Consensus size: 22
75655 CTATTTTAAA
*
75665 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
75687 A-TT-TTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
75707 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
*
75728 ATTTTATTTTAAAATAT-GTTTG
1 A-TTTATTTTAAAATATGGATTG
* * ***
75750 CTTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
75772 ATTTATTTT-AAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
75793 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
75815 ATTTATTTTAAAATATAGATTA
1 ATTTATTTTAAAATATGGATTG
* ***
75837 ATTTA-TTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
75858 ATTTATTTT-AAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
75879 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* * * **
75901 ATTTATTTTATTATTTTAAAATATG
1 ATTTATTTTA-AAATAT-GGAT-TG
*
75926 AATTGATTATTTAAAATATGGATTG
1 -ATTTA-T-TTTAAAATATGGATTG
**
75951 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
*
75972 AATT-TTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
75993 ATTTATTTTAAAATATGGACTG
1 ATTTATTTTAAAATATGGATTG
76015 ATTTA-TTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
76036 CTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
76058 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
76080 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
76102 ATTTATTTTAAAA
1 ATTTATTTTAAAA
76115 AATTTATTAT
Statistics
Matches: 359, Mismatches: 52, Indels: 34
0.81 0.12 0.08
Matches are distributed among these distances:
20 31 0.09
21 97 0.27
22 203 0.57
23 4 0.01
24 6 0.02
25 4 0.01
26 6 0.02
27 4 0.01
28 4 0.01
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:75764 original size:43 final size:44
Alignment explanation
Indices: 75665--76114 Score: 492
Period size: 43 Copynumber: 10.3 Consensus size: 44
75655 CTATTTTAAA
* *
75665 ATTTATTTTAAAATATAGATTGA-TT-TTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGGATTG
* *
75707 ATTTATTTTAAAATATGGA-AAATTTTATTTTAAAATAT-GTTTG
1 ATTTATTTTAAAATATGGATTAA-TTTATTTTAAAATATGGATTG
* * ** *
75750 CTTTATTTTAAAATATGAAAAAATTTATTTT-AAATATAGATTG
1 ATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGGATTG
* * *
75793 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATAGATTA
1 ATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGGATTG
* ** *
75837 ATTTA-TTTAAAATATGAAAAAATTTATTTT-AAATATGAATTG
1 ATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGGATTG
*
75879 ATTTATTTTAAAATATGGATTGATTTATTTTATTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATT-A---A---T-TTATTTTAAAATATGGATTG
* **
75931 A-TTA-TTTAAAATATGGATTGATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGGATTG
* * *
75972 AATT-TTTTAAAATATGGATTGATTTATTTTAAAATATGGACTG
1 ATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGGATTG
**
76015 ATTTA-TTTAAAATATGGATTGCTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGGATTG
* *
76058 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGGATTG
76102 ATTTATTTTAAAA
1 ATTTATTTTAAAA
76115 AATTTATTAT
Statistics
Matches: 353, Mismatches: 34, Indels: 40
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.01
42 91 0.26
43 139 0.39
44 80 0.23
46 1 0.00
47 1 0.00
50 16 0.05
51 10 0.03
52 13 0.04
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (44 bp):
ATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGGATTG
Found at i:75916 original size:30 final size:29
Alignment explanation
Indices: 75881--75937 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
75871 ATGAATTGAT
*
75881 TTATTTTAAAATATGGATTGATTTATTTTA
1 TTATTTTAAAATATGAATTGA-TTATTTTA
75911 TTATTTTAAAATATGAATTGATTATTT
1 TTATTTTAAAATATGAATTGATTATTT
75938 AAAATATGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (29 bp):
TTATTTTAAAATATGAATTGATTATTTTA
Found at i:76346 original size:23 final size:23
Alignment explanation
Indices: 76316--76366 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
76306 CTCTTCTACT
*
76316 GCAGATGTTTGTAGAAGTGGTCC
1 GCAGATGTCTGTAGAAGTGGTCC
*
76339 GCAGATGTCTGTAGATGTGGTCC
1 GCAGATGTCTGTAGAAGTGGTCC
76362 GCAGA
1 GCAGA
76367 CTGCAGACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (23 bp):
GCAGATGTCTGTAGAAGTGGTCC
Found at i:76569 original size:24 final size:25
Alignment explanation
Indices: 76540--76597 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
76530 ATTACAAAAT
76540 TAATTTTAAACATATTAT-TTTAAA
1 TAATTTTAAACATATTATATTTAAA
* * *
76564 TAATTTGAGATATATTATATTTAAA
1 TAATTTTAAACATATTATATTTAAA
*
76589 AATATTTTA
1 TA-ATTTTA
76598 TTATTGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 15 0.56
25 7 0.26
26 5 0.19
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (25 bp):
TAATTTTAAACATATTATATTTAAA
Found at i:79125 original size:19 final size:18
Alignment explanation
Indices: 79090--79152 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
79080 TTATATTTAT
*
79090 TATTAAATAA-AAGTATAA
1 TATTATATAATAA-TATAA
79108 TATTAGTATAATAATAT-A
1 TATTA-TATAATAATATAA
*
79126 -ATTATATCAATAATATAG
1 TATTATAT-AATAATATAA
79144 TATTATATA
1 TATTATATA
79153 TTAAATTATC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 3 0.08
17 12 0.32
18 7 0.18
19 14 0.37
20 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (18 bp):
TATTATATAATAATATAA
Found at i:80104 original size:30 final size:31
Alignment explanation
Indices: 80070--80127 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
80060 AAACTTAAAG
*
80070 AGTTTTACAATAC-GAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
80100 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
80128 CCATACAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:80177 original size:20 final size:21
Alignment explanation
Indices: 80152--80190 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
80142 TAATAAATTA
80152 TTTAAAATAAATC-ATCCAAT
1 TTTAAAATAAATCAATCCAAT
80172 TTTAAAATAAATCAATCCA
1 TTTAAAATAAATCAATCCA
80191 TACTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (21 bp):
TTTAAAATAAATCAATCCAAT
Found at i:80198 original size:52 final size:53
Alignment explanation
Indices: 80142--80434 Score: 220
Period size: 52 Copynumber: 5.5 Consensus size: 53
80132 ACAACTACAA
80142 TAATAAATTATTTAAAATAAATC-ATCCAATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCAATTTTAAAATAAATCAATCCATAC
* **
80194 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAAT-C---CAATTTTAA-AATAAATCAATCCATAC
** * ** * * * *
80251 TTTTAAAATAAAT-CAATCAATACAAT-AAATTATTTAAATAAATC-ATCCATAC
1 TAATAAATTATTTAAAATAAAT-CAATCCAATT-TTAAAATAAATCAATCCATAC
80303 TAAT-AATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCA-ATTTTAAAATAAATCAATCCATAC
*
80356 -AACTACA--A--T---ATAAATCAATCCATATTTTAAAATAAATCAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCA-ATTTTAAAAT--A--AATCAATCCATAC
* *
80407 AAATAAA-TATTTAAAATAAATTAATCCA
1 TAATAAATTATTTAAAATAAATCAATCCA
80435 TACTAATAAA
Statistics
Matches: 188, Mismatches: 27, Indels: 47
0.72 0.10 0.18
Matches are distributed among these distances:
47 24 0.13
49 1 0.01
50 1 0.01
51 32 0.17
52 60 0.32
53 15 0.08
54 3 0.02
56 6 0.03
57 30 0.16
58 16 0.09
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (53 bp):
TAATAAATTATTTAAAATAAATCAATCCAATTTTAAAATAAATCAATCCATAC
Found at i:80279 original size:22 final size:22
Alignment explanation
Indices: 80206--80279 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
80196 ATAAATTATT
80206 TAAAATAAATCAATCCATACAA
1 TAAAATAAATCAATCCATACAA
***
80228 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATACAA
*
80254 TAAAATAAATCAATCAATACAA
1 TAAAATAAATCAATCCATACAA
80276 TAAA
1 TAAA
80280 TTATTTAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
22 19 0.46
23 3 0.07
25 3 0.07
26 16 0.39
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATAAATCAATCCATACAA
Found at i:80291 original size:30 final size:30
Alignment explanation
Indices: 80256--80697 Score: 217
Period size: 30 Copynumber: 16.3 Consensus size: 30
80246 CCATATTTTA
*
80256 AAATAAATCAATCAATACAATAAATTATTT
1 AAATAAATCAATCCATACAATAAATTATTT
80286 AAATAAATC-ATCCATACTAAT-AATTATTT
1 AAATAAATCAATCCATAC-AATAAATTATTT
*
80315 AAAATAAATCAAT-C---C-AT--ATT-TTA
1 -AAATAAATCAATCCATACAATAAATTATTT
*
80338 AAATAAATCAATCCATACAACTACA--A--T
1 AAATAAATCAATCCATACAA-TAAATTATTT
***
80365 --ATAAATCAATCCATATTTTAAA--A--T
1 AAATAAATCAATCCATACAATAAATTATTT
*
80389 AAATCAATCAATCCATACAAATAAA-TATTT
1 AAATAAATCAATCCATAC-AATAAATTATTT
*
80419 AAAATAAATTAATCCATACTAATAAA-TATTT
1 -AAATAAATCAATCCATAC-AATAAATTATTT
80450 AAAATAAATCAAT-C---C-AT--A-T-TTT
1 -AAATAAATCAATCCATACAATAAATTATTT
80472 AAATAAATCAATCCATACTAATAAATTATTT
1 AAATAAATCAATCCATAC-AATAAATTATTT
* * * *
80503 AAAATAAATCAAACTATACACTACA--A--T
1 -AAATAAATCAATCCATACAATAAATTATTT
80530 -AATAAATC-ATCCAT---AT------TTT
1 AAATAAATCAATCCATACAATAAATTATTT
80549 AAATAAATCAATCCATACAATAAATTATTT
1 AAATAAATCAATCCATACAATAAATTATTT
*
80579 AAATAAATCAATCCATACTA-AAATTATTT
1 AAATAAATCAATCCATACAATAAATTATTT
*
80608 AAAATAAATCAAT-C---C-AT--ATT-TTA
1 -AAATAAATCAATCCATACAATAAATTATTT
*
80631 AAAT-AATCAATCCATACTATAAATTATTT
1 AAATAAATCAATCCATACAATAAATTATTT
* *
80660 AAA-ATATC-ATTCATACTAATAAATTATTT
1 AAATAAATCAATCCATAC-AATAAATTATTT
80689 AAAATAAAT
1 -AAATAAAT
80698 TATTTTAAAA
Statistics
Matches: 326, Mismatches: 29, Indels: 113
0.70 0.06 0.24
Matches are distributed among these distances:
19 1 0.00
20 8 0.02
21 26 0.08
22 21 0.06
23 7 0.02
24 17 0.05
25 30 0.09
26 18 0.06
27 10 0.03
28 12 0.04
29 46 0.14
30 63 0.19
31 51 0.16
32 16 0.05
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (30 bp):
AAATAAATCAATCCATACAATAAATTATTT
Found at i:80335 original size:82 final size:84
Alignment explanation
Indices: 80142--80357 Score: 310
Period size: 82 Copynumber: 2.7 Consensus size: 84
80132 ACAACTACAA
80142 TAATAAATTATTTAAAATAAATC-ATCCA-ATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAAT-AATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC-AATAAATTAT
80205 TTAAAATAAATCAATCCATAC
64 TTAAAATAAATCAATCCATAC
*
80226 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCAATACAATAAATTAT
1 TAA-TA-ATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAATAAATTAT
80284 TT-AAATAAATC-ATCCATAC
64 TTAAAATAAATCAATCCATAC
80303 TAATAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAA
1 TAATAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAA
80358 CTACAATATA
Statistics
Matches: 119, Mismatches: 2, Indels: 24
0.82 0.01 0.17
Matches are distributed among these distances:
76 1 0.01
77 10 0.08
78 20 0.17
79 17 0.14
80 25 0.21
82 41 0.34
83 3 0.03
84 2 0.02
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (84 bp):
TAATAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAATAAATTATTT
AAAATAAATCAATCCATAC
Found at i:80338 original size:22 final size:22
Alignment explanation
Indices: 80312--80397 Score: 118
Period size: 22 Copynumber: 3.8 Consensus size: 22
80302 CTAATAATTA
80312 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
80334 TTTAAAATAAATCAATCCATACA
1 TTTAAAATAAATCAATCCATA-T
**
80357 ACTACAATATAAATCAATCCATAT
1 TTTA-AA-ATAAATCAATCCATAT
80381 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
80398 AATCCATACA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
22 32 0.58
23 4 0.07
24 4 0.07
25 15 0.27
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:80436 original size:31 final size:31
Alignment explanation
Indices: 80389--80697 Score: 148
Period size: 31 Copynumber: 11.3 Consensus size: 31
80379 ATTTTAAAAT
*
80389 AAATCAATCAATCCATACAAATAAATATTTA
1 AAATAAATCAATCCATACAAATAAATATTTA
* *
80420 AAATAAATTAATCCATACTAATAAATATTTA
1 AAATAAATCAATCCATACAAATAAATATTTA
80451 AAATAAATCAAT-C---C--AT--AT-TTT-
1 AAATAAATCAATCCATACAAATAAATATTTA
*
80472 AAATAAATCAATCCATACTAATAAATTATTTA
1 AAATAAATCAATCCATACAAATAAA-TATTTA
* * * *
80504 AAATAAATCAAACTATAC-ACTACA-A--T-
1 AAATAAATCAATCCATACAAATAAATATTTA
*
80530 -AATAAATC-ATCCAT---AT------TTT-
1 AAATAAATCAATCCATACAAATAAATATTTA
80549 AAATAAATCAATCCATAC-AATAAATTATTT-
1 AAATAAATCAATCCATACAAATAAA-TATTTA
* *
80579 AAATAAATCAATCCATACTAA-AATTATTTA
1 AAATAAATCAATCCATACAAATAAATATTTA
80609 AAATAAATCAAT-C---C--AT--AT-TTTA
1 AAATAAATCAATCCATACAAATAAATATTTA
*
80631 AAAT-AATCAATCCATAC-TATAAATTATTTA
1 AAATAAATCAATCCATACAAATAAA-TATTTA
* *
80661 AAAT--ATC-ATTCATACTAATAAATTATTTA
1 AAATAAATCAATCCATACAAATAAA-TATTTA
80690 AAATAAAT
1 AAATAAAT
80698 TATTTTAAAA
Statistics
Matches: 223, Mismatches: 16, Indels: 78
0.70 0.05 0.25
Matches are distributed among these distances:
19 1 0.00
20 8 0.04
21 25 0.11
22 14 0.06
23 4 0.02
24 5 0.02
25 12 0.05
26 3 0.01
27 4 0.02
28 8 0.04
29 28 0.13
30 45 0.20
31 50 0.22
32 16 0.07
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (31 bp):
AAATAAATCAATCCATACAAATAAATATTTA
Found at i:80446 original size:104 final size:101
Alignment explanation
Indices: 80154--80444 Score: 292
Period size: 104 Copynumber: 2.8 Consensus size: 101
80144 ATAAATTATT
80154 TAAAATAAATC-ATCCA-ATTTTAAAAT--A-AATCAATCCATACTAATAAATTATTTAAAATAA
1 TAAAATAAATCAATCCATATTTTAAAATAAATAATCAATCCATACTAATAAA-TATTTAAAATAA
***
80214 ATCAATCCATAC-AACTACAATAATAAATCAATCCATATTT
65 ATCAATCCATACTAA-T--AA-AATAAATCAATCCATAAAC
* *** *
80254 TAAAATAAATCAATCAATACAATAAATTATTTAAATAAATC-ATCCATACTAATAATTATTTAAA
1 TAAAATAAATCAATCCATATTTTAAA--A--TAAAT-AATCAATCCATACTAATAAATATTTAAA
**
80318 ATAAATCAATCCATA-TTTTAAAATAAATCAATCCATACAAC
61 ATAAATCAATCCATACTAATAAAATAAATCAATCCATA-AAC
*
80359 TACAATATAAATCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATAAATATTTAAAAT
1 TA-AA-ATAAATCAATCCATATTTTAAAATAAAT-AATCAATCCATACTAATAAATATTTAAAAT
*
80424 AAATTAATCCATACTAATAAA
63 AAATCAATCCATACTAATAAA
80445 TATTTAAAAT
Statistics
Matches: 155, Mismatches: 20, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
100 11 0.07
101 4 0.03
102 5 0.03
103 9 0.06
104 52 0.34
105 10 0.06
106 3 0.02
107 19 0.12
108 24 0.15
109 14 0.09
110 4 0.03
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (101 bp):
TAAAATAAATCAATCCATATTTTAAAATAAATAATCAATCCATACTAATAAATATTTAAAATAAA
TCAATCCATACTAATAAAATAAATCAATCCATAAAC
Found at i:80468 original size:21 final size:21
Alignment explanation
Indices: 80444--80488 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
80434 ATACTAATAA
80444 ATATTTAAAATAAATCAATCC
1 ATATTTAAAATAAATCAATCC
*
80465 ATATTTTAAATAAATCAATCC
1 ATATTTAAAATAAATCAATCC
80486 ATA
1 ATA
80489 CTAATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATTTAAAATAAATCAATCC
Found at i:80572 original size:21 final size:21
Alignment explanation
Indices: 80451--80573 Score: 66
Period size: 21 Copynumber: 6.2 Consensus size: 21
80441 TAAATATTTA
***
80451 AAATAAATCAATCCATATTTT
1 AAATAAATCAATCCATACAAT
80472 AAATAAATCAATCCATAC--T
1 AAATAAATCAATCCATACAAT
* * *
80491 -AATAAAT-TAT--TTAAAAT
1 AAATAAATCAATCCATACAAT
* *
80508 AAATCAAA-CTATACACTACAAT
1 AAAT-AAATCAATCCA-TACAAT
***
80530 -AATAAATC-ATCCATATTTT
1 AAATAAATCAATCCATACAAT
80549 AAATAAATCAATCCATACAAT
1 AAATAAATCAATCCATACAAT
80570 AAAT
1 AAAT
80574 TATTTAAATA
Statistics
Matches: 78, Mismatches: 13, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
15 2 0.03
17 3 0.04
18 10 0.13
19 10 0.13
20 15 0.19
21 33 0.42
22 5 0.06
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAAATCAATCCATACAAT
Found at i:80638 original size:21 final size:22
Alignment explanation
Indices: 80605--80646 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
80595 ACTAAAATTA
80605 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
80627 TTTAAAAT-AATCAATCCATA
1 TTTAAAATAAATCAATCCATA
80647 CTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:80653 original size:21 final size:22
Alignment explanation
Indices: 80607--80653 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
80597 TAAAATTATT
* *
80607 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATACTA
80629 TAAAAT-AATCAATCCATACTA
1 TAAAATAAATCAATCCATACTA
80650 TAAA
1 TAAA
80654 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAAATCAATCCATACTA
Found at i:80677 original size:186 final size:187
Alignment explanation
Indices: 80156--80697 Score: 578
Period size: 186 Copynumber: 2.9 Consensus size: 187
80146 AAATTATTTA
80156 AAATAAATCATCCAATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1 AAATAAATCATCCAATTTT-AAATAAATCAATCCATAC-AATAAATTATTT-AAATAAATCAATC
* *
80221 CATAC--AACTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATCAATACAATAAATT
63 CATACAAAAATATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCAATACAATAAATT
* ***
80282 ATTTAAATAAATCATCCATACTAAT-AATTATTTAAAATAAATCAATCCATATTTTAAAAT
127 ATTTAAATAAATCATCCATACTAATAAATTATTTAAAATAAATCAAACCATACACTAAAAT
* * * ** *** *
80342 AAATCAATCCATACAACTACAATATAAATCAATCCATATTTTAAA--A--TAAATCAATCAATCC
1 AAATAAAT-CATCCAATTTTAA-ATAAATCAATCCATACAATAAATTATTTAAATAAATCAATCC
* ** * *
80403 ATACAAATAAATATTTAAAATAAATTAATCCATACTAATAAATATTTAAAATAAATCAAT-CCAT
64 ATAC-AA-AAATATTTAAAATAAATCAATCCATA-TTTTAAA-A--T-AAATCAATCAATACAAT
* *
80467 --A-T-TTTAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAACTATACACTACA
122 AAATTATTTAAATAAATC-ATCCATACTAATAAATTATTTAAAATAAATCAAACCATACACTAAA
80528 AT
186 AT
80530 -AATAAATCATCCATATTTTAAATAAATCAATCCATACAATAAATTATTTAAATAAATCAATCCA
1 AAATAAATCATCCA-ATTTTAAATAAATCAATCCATACAATAAATTATTTAAATAAATCAATCCA
* * *
80594 TACTAAAATTATTTAAAATAAATCAATCCATATTTTAAAAT-AATCAATCCATACTATAAATTAT
65 TAC-AAAAATATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATACAATAAATTAT
* *
80658 TTAAA-ATATCATTCATACTAATAAATTATTTAAAATAAAT
129 TTAAATAAATCATCCATACTAATAAATTATTTAAAATAAAT
80698 TATTTTAAAA
Statistics
Matches: 290, Mismatches: 41, Indels: 50
0.76 0.11 0.13
Matches are distributed among these distances:
181 17 0.06
182 1 0.00
183 9 0.03
184 4 0.01
185 5 0.02
186 94 0.32
187 58 0.20
188 43 0.15
189 24 0.08
190 24 0.08
191 11 0.04
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (187 bp):
AAATAAATCATCCAATTTTAAATAAATCAATCCATACAATAAATTATTTAAATAAATCAATCCAT
ACAAAAATATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATACAATAAATTATTT
AAATAAATCATCCATACTAATAAATTATTTAAAATAAATCAAACCATACACTAAAAT
Found at i:80706 original size:15 final size:15
Alignment explanation
Indices: 80677--80833 Score: 173
Period size: 15 Copynumber: 10.5 Consensus size: 15
80667 CATTCATACT
80677 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
80691 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
80706 AATAAATCAATCCATATTTTA
1 AATAAAT---T--AT-TTTAA
*
80727 TA-AAATTATTTT-A
1 AATAAATTATTTTAA
80740 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
80755 AATAAATTA-TTTAT
1 AATAAATTATTTTAA
80769 AAT-AATTATTTTAA
1 AATAAATTATTTTAA
* *
80783 AATAACTTATTATAA
1 AATAAATTATTTTAA
80798 AATAAATTATTTTAA
1 AATAAATTATTTTAA
80813 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
80827 AATAAAT
1 AATAAAT
80834 AACCTTATTA
Statistics
Matches: 123, Mismatches: 9, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
13 7 0.06
14 48 0.39
15 55 0.45
17 1 0.01
18 1 0.01
20 6 0.05
21 5 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:80737 original size:49 final size:48
Alignment explanation
Indices: 80599--80761 Score: 156
Period size: 49 Copynumber: 3.4 Consensus size: 48
80589 ATCCATACTA
* * * **
80599 AAATTATTTAAAATAAATCAATCCATATTTTAAAATAATCAATCCATACTAT
1 AAATTATTTAAAATAAATCAATCCATATTTTATAA-AAT-TAT--TTAAAAT
* * *
80651 AAATTATTTAAAAT--ATC-ATTCATA-CTAAT-AAATTATTTAAAAT
1 AAATTATTTAAAATAAATCAATCCATATTTTATAAAATTATTTAAAAT
*
80694 AAATTATTTTAAAATAAATCAATCCATATTTTATAAAATTATTTTAAAT
1 AAATTA-TTTAAAATAAATCAATCCATATTTTATAAAATTATTTAAAAT
80743 AAATTATTTTAAAATAAAT
1 AAATTA-TTTAAAATAAAT
80762 TATTTATAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
43 10 0.11
44 8 0.09
45 2 0.02
46 6 0.06
47 7 0.08
48 5 0.05
49 38 0.41
50 3 0.03
52 14 0.15
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (48 bp):
AAATTATTTAAAATAAATCAATCCATATTTTATAAAATTATTTAAAAT
Done.