Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008559.1 Hibiscus syriacus cultivar Beakdansim tig00111466_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: 490547
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 3
Found at i:415 original size:94 final size:93
Alignment explanation
Indices: 196--512 Score: 582
Period size: 93 Copynumber: 3.4 Consensus size: 93
186 TTAGATGCTT
* *
196 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAATAGTA
261 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
289 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAATAGTA
354 TTTGGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTT-GTCTTTGTTTTGTCTTTTGGTTGAA
*
383 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAATAGTA
448 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
476 AGTAAATTTGTTCGG-TGCTGTCAATTCTGCTAAACTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTA
513 ATAACCTGAA
Statistics
Matches: 218, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
92 20 0.09
93 106 0.49
94 92 0.42
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:696 original size:19 final size:19
Alignment explanation
Indices: 672--730 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
662 GCAACGACAG
672 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
691 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
*
705 AATCGCAACGCAAAACCAA
1 AATCGCAACGCGAAACCAA
724 AATCGCA
1 AATCGCA
731 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 11 0.32
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 18 0.53
ACGTcount: A:0.49, C:0.31, G:0.14, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:699 original size:33 final size:33
Alignment explanation
Indices: 608--730 Score: 167
Period size: 33 Copynumber: 3.7 Consensus size: 33
598 TAGTTTACTT
* * *
608 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
642 TCGCAACGCGAAA-TGAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
674 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
707 TCGCAACGCAAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
731 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
32 30 0.37
33 39 0.48
34 12 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:707 original size:14 final size:14
Alignment explanation
Indices: 624--719 Score: 68
Period size: 14 Copynumber: 6.3 Consensus size: 14
614 CACGAAACTT
*
624 AAAATCGCAACGAG
1 AAAATCGCAACGAC
* *
638 AGAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
654 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
670 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
689 AAAATCGCAACGAC
1 AAAATCGCAACGAC
703 AAAATCGCAACG-C
1 AAAATCGCAACGAC
716 AAAA
1 AAAA
720 CCAAAATCGC
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
13 5 0.07
14 30 0.45
15 1 0.01
16 10 0.15
17 2 0.03
18 9 0.13
19 10 0.15
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:748 original size:19 final size:19
Alignment explanation
Indices: 726--867 Score: 161
Period size: 19 Copynumber: 7.8 Consensus size: 19
716 AAAACCAAAA
*
726 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
745 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
764 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
780 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
797 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
816 TCGCGTTGCGA-TTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
834 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
853 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
868 AAGTTTCGTG
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
14 7 0.07
16 5 0.05
17 5 0.05
18 17 0.16
19 70 0.67
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:793 original size:52 final size:53
Alignment explanation
Indices: 731--867 Score: 188
Period size: 52 Copynumber: 2.5 Consensus size: 53
721 CAAAATCGCA
731 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCT-G-TCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATT-TGGTTCG
** *
783 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTGG--T-TCG
*
839 TTGCGATTCTCATTTCGCGTTGCGATTTT
1 TTGCGATTTTCATTTCGCGTTGCGATTTT
868 AAGTTTCGTG
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
51 1 0.01
52 44 0.58
56 31 0.41
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.47
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTGGTTCG
Found at i:1971 original size:16 final size:17
Alignment explanation
Indices: 1950--1984 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1940 ACTATTACGA
1950 TTTATGATTG-AGGTGT
1 TTTATGATTGCAGGTGT
1966 TTTATGATTGCAGGTGT
1 TTTATGATTGCAGGTGT
1983 TT
1 TT
1985 ATCCCTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.17, C:0.03, G:0.29, T:0.51
Consensus pattern (17 bp):
TTTATGATTGCAGGTGT
Found at i:2730 original size:14 final size:14
Alignment explanation
Indices: 2711--2746 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2701 ACTGTTTAAT
2711 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2725 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2739 TGATTTGT
1 TGATTTGT
2747 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2928 original size:20 final size:19
Alignment explanation
Indices: 2855--2950 Score: 130
Period size: 20 Copynumber: 5.2 Consensus size: 19
2845 AATGACTATT
2855 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
2874 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
2893 GCAA--CG--A-GAGAATC
1 GCAATGCGAAATGAAAATC
2907 GCAATGCGGAAATGAAAATC
1 GCAATGC-GAAATGAAAATC
2927 GCAATGCGGAAATGAAAATC
1 GCAATGC-GAAATGAAAATC
2947 GCAA
1 GCAA
2951 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 3 0.04
19 24 0.35
20 30 0.43
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.14
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATC
Found at i:2954 original size:54 final size:53
Alignment explanation
Indices: 2855--2968 Score: 212
Period size: 54 Copynumber: 2.2 Consensus size: 53
2845 AATGACTATT
2855 GCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATC
1 GCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATC
2907 GCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATC
1 GCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATC
2961 GCAATGCG
1 GCAATGCG
2969 ATTTTCATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 7 0.12
53 19 0.32
54 34 0.57
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (53 bp):
GCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATC
Found at i:3108 original size:72 final size:71
Alignment explanation
Indices: 2960--3192 Score: 248
Period size: 72 Copynumber: 3.2 Consensus size: 71
2950 ACGAGAGAAT
* * * * * *
2960 CGCAATGCGATTTTCATTTCGCATTGCGATT-TTCATTTCCGCA-TTGCGATTCTCTCGTTGCGA
1 CGCATTGCGATTTTCATTTCGCATTGCGATTCTTC-GTTGCG-ATTTTC-ATT-TCGCATTGCGA
3023 TTTTCATTT-
62 TTTTCATTTC
3032 CGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTT
1 CGCATTGCGATTTTCATTTCGCATTGCGATTCT-TCGTTGCGATTTTCATTTCGCATTGCGATTT
3097 TCATTTC
65 TCATTTC
*
3104 CGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 CGCATTGCGATTTTCATTTCGCATTGCGA--TTC--TTCG--TTGCGATTTTCATTTCGCATTGC
3164 GATTTTCATTTC
60 GATTTTCATTTC
3176 CGCATTGCGATTTTCAT
1 CGCATTGCGATTTTCAT
3193 GTTGGGATTT
Statistics
Matches: 141, Mismatches: 7, Indels: 23
0.82 0.04 0.13
Matches are distributed among these distances:
67 6 0.04
69 7 0.05
70 6 0.04
71 19 0.13
72 89 0.63
73 8 0.06
74 5 0.04
75 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (71 bp):
CGCATTGCGATTTTCATTTCGCATTGCGATTCTTCGTTGCGATTTTCATTTCGCATTGCGATTTT
CATTTC
Found at i:3127 original size:105 final size:109
Alignment explanation
Indices: 2965--3234 Score: 434
Period size: 105 Copynumber: 2.6 Consensus size: 109
2955 AGAATCGCAA
2965 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
3030 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TAT-CG-T
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATATCCGAT
3070 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
3135 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATATCCG-AT
*
3181 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
3235 GTAATTTCCG
Statistics
Matches: 157, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
105 122 0.78
106 14 0.09
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATATCCGAT
Found at i:3202 original size:72 final size:72
Alignment explanation
Indices: 2987--3220 Score: 288
Period size: 72 Copynumber: 3.3 Consensus size: 72
2977 TTCGCATTGC
*
2987 GATTTTCATTTCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGATTTT
1 GATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTT
*
3046 CAT-TTCG
65 CATGTTGG
* * ** * *
3053 CA-TTGCGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTC
1 GATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT
*
3117 TC-TCGTTGC
64 TCAT-GTTGG
3126 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
3191 ATGTTGG
66 ATGTTGG
3198 GATTTTCATTTCGCATTGCGATT
1 GATTTTCATTTCGCATTGCGATT
3221 CTCTCGTTGC
Statistics
Matches: 140, Mismatches: 16, Indels: 18
0.80 0.09 0.10
Matches are distributed among these distances:
65 3 0.02
66 11 0.08
67 1 0.01
68 3 0.02
69 4 0.03
71 16 0.11
72 92 0.66
73 7 0.05
74 3 0.02
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (72 bp):
GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
ATGTTGG
Found at i:3249 original size:53 final size:52
Alignment explanation
Indices: 2965--3234 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
2955 AGAATCGCAA
2965 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
3018 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
3070 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
3123 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
3181 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
3228 TGCGATT
1 TGCGATT
3235 GTAATTTCCG
Statistics
Matches: 205, Mismatches: 5, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 61 0.30
53 108 0.53
54 3 0.01
55 3 0.01
56 3 0.01
58 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:5524 original size:12 final size:12
Alignment explanation
Indices: 5507--5531 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5497 TCTTCGGGGA
5507 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5519 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5531 C
1 C
5532 AAGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:6470 original size:20 final size:20
Alignment explanation
Indices: 6442--6670 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
6432 AAATTTCAGT
* * *
6442 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
6462 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
6482 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
6502 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
6522 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
6542 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
6562 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
6582 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
6602 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
6622 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
6642 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
6662 GTTGCGATT
1 GTTGCGATT
6671 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:8131 original size:20 final size:21
Alignment explanation
Indices: 8092--8131 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
8082 AGCGCTACCT
*
8092 AAAATATTATTTTTTCTATCG
1 AAAATATTATATTTTCTATCG
*
8113 AAAATATTA-ATTTTGTATC
1 AAAATATTATATTTTCTATC
8132 TAATTTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
AAAATATTATATTTTCTATCG
Found at i:8492 original size:50 final size:50
Alignment explanation
Indices: 8431--8554 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 50
8421 TTAGCAGAAA
* *
8431 AGCGCGCCCCCTGCACCGCGCTATATGCTGATTTGACGT-CACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGCTGATCTGAC-TCCACGTGGGTAT
* * * * *
8481 AGTGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCTCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGCTGATCTGACTCCACGTGGGTAT
*
8531 AGCGCGCCCCTTG-ATCCGCGCTAT
1 AGCGCGCCCCCTGCA-CCGCGCTAT
8555 CCCTGGATAT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
49 1 0.02
50 60 0.98
ACGTcount: A:0.15, C:0.35, G:0.28, T:0.23
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGCTGATCTGACTCCACGTGGGTAT
Found at i:8973 original size:111 final size:111
Alignment explanation
Indices: 8840--9061 Score: 374
Period size: 111 Copynumber: 2.0 Consensus size: 111
8830 TGGAAATCAT
* *
8840 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTTAATTATAAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATAAGTAA
* * *
8905 TATTTAGTTGATTTA-TTATGTGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTA-ATGCATGATTATTAGATTAAGAATTAA
*
8951 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATAAGTAA
9016 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
9062 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
111 101 0.97
112 3 0.03
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATAAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:10592 original size:18 final size:18
Alignment explanation
Indices: 10569--10608 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
10559 CCAGCAGCCA
10569 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
10587 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
10605 CCGC
1 CCGC
10609 TATCGCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:14946 original size:50 final size:50
Alignment explanation
Indices: 14859--14956 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 50
14849 GATCGGGGGG
* * * * *
14859 GCTATACCCACGTGGCGCCAGATCACCGTATATCGCGGGGCAGGGGGCGC
1 GCTATACCCACGTGACGCCAAATCAACATATAGCGCGGGGCAGGGGGCGC
* * *
14909 GCTATACCCACGTGACGCTAAATCAACATATAGCGCGGTGTAGGGGGC
1 GCTATACCCACGTGACGCCAAATCAACATATAGCGCGGGGCAGGGGGC
14957 ACACTTTTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (50 bp):
GCTATACCCACGTGACGCCAAATCAACATATAGCGCGGGGCAGGGGGCGC
Found at i:15159 original size:20 final size:20
Alignment explanation
Indices: 15136--15180 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
15126 ATCATTTTAA
*
15136 ATTTTGATGTGACATTTGTG
1 ATTTTGATGTGACATTTATG
*
15156 ATTTTGATGTGACGTTTATG
1 ATTTTGATGTGACATTTATG
15176 ATTTT
1 ATTTT
15181 CACGATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.53
Consensus pattern (20 bp):
ATTTTGATGTGACATTTATG
Found at i:15673 original size:20 final size:20
Alignment explanation
Indices: 15650--15877 Score: 161
Period size: 20 Copynumber: 11.3 Consensus size: 20
15640 AATATGTAAA
*
15650 TCGCAACACAGAAGTCAAAT
1 TCGCAACACTGAAGTCAAAT
* *
15670 TCGCAAC-GTGATAGTTAAAT
1 TCGCAACACTGA-AGTCAAAT
15690 TCGCAACACTGAAGTCAAAT
1 TCGCAACACTGAAGTCAAAT
**
15710 TCGCAACACAAAAGTCAAAT
1 TCGCAACACTGAAGTCAAAT
*
15730 TCGCAAC-GTGATAGTCAAAT
1 TCGCAACACTGA-AGTCAAAT
* *
15750 TCGTAAC-GTGAA-TCTGTAAA-
1 TCGCAACACTGAAGTC---AAAT
*
15770 TCGCAACGC-GAATTTGT-AAA-
1 TCGCAACACTGAA---GTCAAAT
*
15790 TCGCAACACAGAAGTCAAAT
1 TCGCAACACTGAAGTCAAAT
* *
15810 TCGCAACA-AGATGGTCAAAT
1 TCGCAACACTGA-AGTCAAAT
*
15830 TCGCAACACTGAATTTC-AAT
1 TCGCAACACTGAA-GTCAAAT
*
15850 TCGCAACACTGAATTTCAAAT
1 TCGCAACACTGAA-GTCAAAT
15871 TCGCAAC
1 TCGCAAC
15878 TCGATTTTCG
Statistics
Matches: 172, Mismatches: 18, Indels: 35
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.02
19 10 0.06
20 134 0.78
21 23 0.13
24 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (20 bp):
TCGCAACACTGAAGTCAAAT
Found at i:15774 original size:60 final size:59
Alignment explanation
Indices: 15625--15776 Score: 191
Period size: 60 Copynumber: 2.5 Consensus size: 59
15615 ACTCAGTTTC
* * *
15625 CAAATTCACAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGTGAAT-TGTAAATCGCAACACAAAAGTCAAATTCGCAACGTGATAGT
* *
15685 TAAATTCGCAACACTGAA--GTCAAATTCGCAACACAAAAGTCAAATTCGCAACGTGATAGT
1 CAAATTCGCAAC-GTGAATTGT-AAA-TCGCAACACAAAAGTCAAATTCGCAACGTGATAGT
*
15745 CAAATTCGTAACGTGAATCTGTAAATCGCAAC
1 CAAATTCGCAACGTGAAT-TGTAAATCGCAAC
15777 GCGAATTTGT
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
58 2 0.03
59 7 0.09
60 61 0.78
61 6 0.08
62 2 0.03
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (59 bp):
CAAATTCGCAACGTGAATTGTAAATCGCAACACAAAAGTCAAATTCGCAACGTGATAGT
Found at i:15886 original size:20 final size:21
Alignment explanation
Indices: 15650--15905 Score: 143
Period size: 20 Copynumber: 12.8 Consensus size: 21
15640 AATATGTAAA
* *
15650 TCGCAACACAGAA-GTCAAAT
1 TCGCAACACTGAATTTCAAAT
* *
15670 TCGCAAC-GTGATAGTT-AAAT
1 TCGCAACACTGA-ATTTCAAAT
*
15690 TCGCAACACTGAA-GTCAAAT
1 TCGCAACACTGAATTTCAAAT
* **
15710 TCGCAACAC-AAAAGTCAAAT
1 TCGCAACACTGAATTTCAAAT
* *
15730 TCGCAAC-GTG-ATAGTCAAAT
1 TCGCAACACTGAAT-TTCAAAT
* *
15750 TCGTAAC-GTGAATCTGT-AAA-
1 TCGCAACACTGAAT-T-TCAAAT
* *
15770 TCGCAACGC-GAATTTGTAAA-
1 TCGCAACACTGAATTT-CAAAT
* *
15790 TCGCAACACAGAA-GTCAAAT
1 TCGCAACACTGAATTTCAAAT
* *
15810 TCGCAACA-AG-ATGGTCAAAT
1 TCGCAACACTGAAT-TTCAAAT
15830 TCGCAACACTGAATTTC-AAT
1 TCGCAACACTGAATTTCAAAT
15850 TCGCAACACTGAATTTCAAAT
1 TCGCAACACTGAATTTCAAAT
* * *
15871 TCGCAACTC-GATTTTCGAAT
1 TCGCAACACTGAATTTCAAAT
15891 TCGCAACAC-GAATTT
1 TCGCAACACTGAATTT
15906 AATTTCGTAA
Statistics
Matches: 193, Mismatches: 24, Indels: 38
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.01
19 12 0.06
20 150 0.78
21 26 0.13
22 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (21 bp):
TCGCAACACTGAATTTCAAAT
Found at i:19142 original size:18 final size:18
Alignment explanation
Indices: 19119--19154 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19109 AAGAAAAAGG
*
19119 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
19137 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
19155 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:19578 original size:14 final size:14
Alignment explanation
Indices: 19561--19594 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
19551 AAATTAAACT
19561 AATCAACTTTTACA
1 AATCAACTTTTACA
19575 AATCAACTTTTACA
1 AATCAACTTTTACA
19589 AATCAA
1 AATCAA
19595 TTAAACAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:21031 original size:21 final size:21
Alignment explanation
Indices: 20983--21101 Score: 98
Period size: 21 Copynumber: 5.7 Consensus size: 21
20973 GTGAATCGGG
* *
20983 CTCTTGAACAGTGAGAGGGAC
1 CTCTTGAACAATGAGAGGGGC
*
21004 C-CATTGAACAATGACAGGGGC
1 CTC-TTGAACAATGAGAGGGGC
** *
21025 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACAATGAGAGGGGC
* *
21046 CTCTTGAACGATGAGAGGAGC
1 CTCTTGAACAATGAGAGGGGC
* * *
21067 CTCTTGAACGAT-AGGAGGCGT
1 CTCTTGAACAATGA-GAGGGGC
*
21088 CTCTTGAACGATGA
1 CTCTTGAACAATGA
21102 CAGGTGAATC
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.02
21 78 0.95
22 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.34, T:0.20
Consensus pattern (21 bp):
CTCTTGAACAATGAGAGGGGC
Found at i:21043 original size:42 final size:42
Alignment explanation
Indices: 20983--21076 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
20973 GTGAATCGGG
* *
20983 CTCTTGAACAGTGAGAGGGACC-CATTGAACAATGACAGGGGC
1 CTCTTGAACGGTGAGAGGGACCTC-TTGAACAATGACAGGAGC
* * * *
21025 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGAGC
1 CTCTTGAACGGTGAGAGGGACCTCTTGAACAATGACAGGAGC
21067 CTCTTGAACG
1 CTCTTGAACG
21077 ATAGGAGGCG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 44 0.98
43 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.34, T:0.19
Consensus pattern (42 bp):
CTCTTGAACGGTGAGAGGGACCTCTTGAACAATGACAGGAGC
Found at i:21084 original size:42 final size:42
Alignment explanation
Indices: 21007--21105 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
20997 GAGGGACCCA
* * * * *
21007 TTGAACAATGACAGGGGCCTCTTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGACAGGAGCCTCTTGAACGATAGGAGGCGCCTC
* *
21049 TTGAACGATGAGAGGAGCCTCTTGAACGATAGGAGGCGTCTC
1 TTGAACGATGACAGGAGCCTCTTGAACGATAGGAGGCGCCTC
21091 TTGAACGATGACAGG
1 TTGAACGATGACAGG
21106 TGAATCGAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.20
Consensus pattern (42 bp):
TTGAACGATGACAGGAGCCTCTTGAACGATAGGAGGCGCCTC
Found at i:21277 original size:4 final size:4
Alignment explanation
Indices: 21245--21294 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
21235 GGGCCGTTGA
* * * *
21245 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
21293 AA
1 AA
21295 TGCCGAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:21492 original size:63 final size:63
Alignment explanation
Indices: 21425--21564 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 63
21415 TTAAAGTAGA
* *
21425 TACCTCATCACGTAGTGCACCATTGTCATCGCGTAAAACATCCACCTCACCACGTAAAG-ACCG
1 TACCTCATCACGTA-TGCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCG
** * ** * **
21488 TACCTCATCACACCATGCACCATTGTCTTCACGTAAAGTATCGACCTCATGACGCAAAGCACCG
1 TACCTCATCAC-GTATGCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCG
21552 -ACCTCATCACGTA
1 TACCTCATCACGTA
21565 ACTCCCCTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
62 1 0.02
63 57 0.90
64 5 0.08
ACGTcount: A:0.30, C:0.35, G:0.14, T:0.21
Consensus pattern (63 bp):
TACCTCATCACGTATGCACCATTGTCATCACGTAAAACATCCACCTCACCACGCAAAGCACCG
Found at i:23304 original size:20 final size:20
Alignment explanation
Indices: 23279--23316 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23269 TTCGCAACGA
23279 GAAAATCGCAACGCGAAAAT
1 GAAAATCGCAACGCGAAAAT
*
23299 GAAAATCGCAACTCGAAA
1 GAAAATCGCAACGCGAAA
23317 CTAAAATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (20 bp):
GAAAATCGCAACGCGAAAAT
Found at i:23931 original size:20 final size:20
Alignment explanation
Indices: 23901--24074 Score: 142
Period size: 20 Copynumber: 8.7 Consensus size: 20
23891 AATAAAATTT
*
23901 GTGTTGAGAATTTGACTTTC
1 GTGTTGCGAATTTGACTTTC
*
23921 GCGTTGCGAATTTGAC-TTC
1 GTGTTGCGAATTTGACTTTC
* *
23940 TGTGTTGTGAATTTGACTTTT
1 -GTGTTGCGAATTTGACTTTC
* *
23961 GTGTTACG-ATTT-ACAAATTC
1 GTGTTGCGAATTTGAC--TTTC
* *
23981 GCGTTGCGAA-TTGACTTTTT
1 GTGTTGCGAATTTGAC-TTTC
* * *
24001 GTATTGCGAATTTAACTTTT
1 GTGTTGCGAATTTGACTTTC
*
24021 GTGTTGCGAATTTGACTATC
1 GTGTTGCGAATTTGACTTTC
* *
24041 GCGTTGCGAATTTAAC-TTC
1 GTGTTGCGAATTTGACTTTC
24060 TGTGTTGCGAATTTG
1 -GTGTTGCGAATTTG
24075 GAAACTGGGT
Statistics
Matches: 120, Mismatches: 26, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
18 2 0.02
19 9 0.08
20 100 0.83
21 9 0.08
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (20 bp):
GTGTTGCGAATTTGACTTTC
Found at i:23955 original size:40 final size:40
Alignment explanation
Indices: 23900--24074 Score: 185
Period size: 40 Copynumber: 4.4 Consensus size: 40
23890 AAATAAAATT
* *
23900 TGTGTTGAGAATTTGACTTTCGCGTTGCGAATTTGACTTC
1 TGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTAACTTC
* * * * *
23940 TGTGTTGTGAATTTGACTTTTGTGTTACG-ATTTACAAATTC
1 TGTGTTGCGAATTTGACTTTCGCGTTGCGAATTT--AACTTC
* * ** *
23981 -GCGTTGCGAA-TTGACTTTTTGTATTGCGAATTTAACTTT
1 TGTGTTGCGAATTTGAC-TTTCGCGTTGCGAATTTAACTTC
*
24020 TGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTC
1 TGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTAACTTC
24060 TGTGTTGCGAATTTG
1 TGTGTTGCGAATTTG
24075 GAAACTGGGT
Statistics
Matches: 111, Mismatches: 18, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
39 13 0.12
40 85 0.77
41 13 0.12
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (40 bp):
TGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTAACTTC
Found at i:23991 original size:60 final size:61
Alignment explanation
Indices: 23898--24074 Score: 213
Period size: 60 Copynumber: 3.0 Consensus size: 61
23888 TAAAATAAAA
* *
23898 TTTGTGTTGA-GAATTTGAC-TTTCGCGTTGCGAATTTGACTTCTGTGTTGTGAATTTGACT
1 TTTGTGTT-ACGAATTTGACAATTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACT
* * *
23958 TTTGTGTTACG-ATTT-ACAAATTCGCGTTGCGAA-TTGACTTTTTGTATTGCGAATTTAACT
1 TTTGTGTTACGAATTTGAC-AATTCGCGTTGCGAATTTGAC-TTCTGTGTTGCGAATTTGACT
* * *
24018 TTTGTGTTGCGAATTTGACTA-TCGCGTTGCGAATTTAACTTCTGTGTTGCGAATTTG
1 TTTGTGTTACGAATTTGACAATTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTG
24075 GAAACTGGGT
Statistics
Matches: 99, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
58 2 0.02
59 10 0.10
60 76 0.77
61 9 0.09
62 2 0.02
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (61 bp):
TTTGTGTTACGAATTTGACAATTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACT
Found at i:24087 original size:60 final size:59
Alignment explanation
Indices: 23900--24115 Score: 183
Period size: 60 Copynumber: 3.6 Consensus size: 59
23890 AAATAAAATT
* * * ***
23900 TGTGTTGAGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGTGAATTTGACTTT
1 TGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGA-AAC
* * * *
23960 TGTGTTACG-ATTT-ACAAATTCGCGTTGCGAA-TTGACTTTTTGTATTGCGAATTT--AAC
1 TGTGTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGAC-TTCTGTGTTGCGAATTTGAAAC
*
24017 TTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCTGTGTTGCGAATTTGGAAAC
1 ---TGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTT-GAAAC
* * *
24080 TGGGTTGCGAAATTGGAGT-TCGCGTTGCGAATTTGA
1 TGTGTTGCG-AATTTGACTATCGCGTTGCGAATTTGA
24116 GATCGCGTTG
Statistics
Matches: 124, Mismatches: 19, Indels: 26
0.73 0.11 0.15
Matches are distributed among these distances:
58 2 0.02
59 9 0.07
60 92 0.74
61 16 0.13
62 2 0.02
63 3 0.02
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.42
Consensus pattern (59 bp):
TGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGAAAC
Found at i:24106 original size:20 final size:19
Alignment explanation
Indices: 24083--24131 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
24073 TGGAAACTGG
*
24083 GTTGCGAAATTGGAGTTCGC
1 GTTGCG-AATTGGAGATCGC
*
24103 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTGGAGATCGC
*
24122 GTTGTGAATT
1 GTTGCGAATT
24132 TGTTGGTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTGGAGATCGC
Found at i:24651 original size:22 final size:24
Alignment explanation
Indices: 24621--24664 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
24611 GTTTGAAATA
24621 TTAAGATATAATAA-ATTTTAACC
1 TTAAGATATAATAATATTTTAACC
*
24644 TTAA-ATATATTAATATTTTAA
1 TTAAGATATAATAATATTTTAA
24665 AATCTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAAGATATAATAATATTTTAACC
Found at i:24841 original size:34 final size:34
Alignment explanation
Indices: 24777--24841 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
24767 CCCAATTGAT
* *
24777 TTTATATTCGTTTGTTTACGTTCGTTTATGTACG
1 TTTATATTCGTTTGTTTACGTTCATGTATGTACG
* **
24811 TTTATGTTCGTTTGTTTGTGTTCATGTATGT
1 TTTATATTCGTTTGTTTACGTTCATGTATGT
24842 TCATTCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.12, C:0.09, G:0.20, T:0.58
Consensus pattern (34 bp):
TTTATATTCGTTTGTTTACGTTCATGTATGTACG
Found at i:27193 original size:26 final size:27
Alignment explanation
Indices: 27157--27231 Score: 120
Period size: 26 Copynumber: 2.9 Consensus size: 27
27147 CGCCATTGCA
*
27157 TGTGCAGCTCGGTTGT-TTTCTCTGGG
1 TGTGCAGCTCGGTTATATTTCTCTGGG
27183 TGTGCAGCTC-GTTATATTTCTCTGGG
1 TGTGCAGCTCGGTTATATTTCTCTGGG
27209 TGTGCAGCTC-GTTATATTTCTCT
1 TGTGCAGCTCGGTTATATTTCTCT
27232 TATGATTGTG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 4 0.09
26 43 0.91
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.44
Consensus pattern (27 bp):
TGTGCAGCTCGGTTATATTTCTCTGGG
Found at i:28915 original size:2 final size:2
Alignment explanation
Indices: 28908--28963 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
28898 TATCAACTTT
28908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28950 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
28964 ATACTTGAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30744 original size:2 final size:2
Alignment explanation
Indices: 30739--30763 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30729 AAGTTAACAA
30739 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
30764 ATTCAACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32150 original size:11 final size:11
Alignment explanation
Indices: 32130--32160 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
32120 AATGGCAACT
32130 GGGCGGGTTCG
1 GGGCGGGTTCG
*
32141 GGGTGGGTTCG
1 GGGCGGGTTCG
32152 GGGCGGGTT
1 GGGCGGGTT
32161 TTGCTCTCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.65, T:0.23
Consensus pattern (11 bp):
GGGCGGGTTCG
Found at i:32345 original size:17 final size:17
Alignment explanation
Indices: 32323--32360 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
32313 CCCGTATTAA
32323 AAAAATAGAAAAAATAT
1 AAAAATAGAAAAAATAT
*
32340 AAAAATATAAAAAATAT
1 AAAAATAGAAAAAATAT
32357 AAAA
1 AAAA
32361 TATTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAATAGAAAAAATAT
Found at i:32389 original size:9 final size:9
Alignment explanation
Indices: 32322--32360 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
32312 ACCCGTATTA
*
32322 AAAAAATAG
1 AAAAAATAT
32331 AAAAAATAT
1 AAAAAATAT
32340 -AAAAATAT
1 AAAAAATAT
32348 AAAAAATAT
1 AAAAAATAT
32357 AAAA
1 AAAA
32361 TATTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (9 bp):
AAAAAATAT
Found at i:32396 original size:33 final size:34
Alignment explanation
Indices: 32343--32406 Score: 121
Period size: 33 Copynumber: 1.9 Consensus size: 34
32333 AAAATATAAA
32343 AATATAAAAAATATAAAATATTATATATATAATT
1 AATATAAAAAATATAAAATATTATATATATAATT
32377 AATATAAAAAATA-AAAATATTATATATATA
1 AATATAAAAAATATAAAATATTATATATATA
32407 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (34 bp):
AATATAAAAAATATAAAATATTATATATATAATT
Found at i:32402 original size:2 final size:2
Alignment explanation
Indices: 32393--32422 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
32383 AAAAATAAAA
32393 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32423 ATCGGGGCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33393 original size:60 final size:59
Alignment explanation
Indices: 33301--33412 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 59
33291 GAACATATGA
* *
33301 ATAGTCGGATGACTCTTTGTAATTTTTAATAGTCGAA-GGACTCAACAAAGCAAAGCTTT
1 ATAGTCGGAGGACTCTTTGTAACTTTTAATAGTC-AATGGACTCAACAAAGCAAAGCTTT
* * *
33360 ATAGTCGGAGGACTATTTTGTAACTTTTAATAGTCAATGGACTTAATAAAGCA
1 ATAGTCGGAGGACT-CTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCA
33413 TTACCCTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
59 15 0.33
60 31 0.67
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (59 bp):
ATAGTCGGAGGACTCTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAAAGCTTT
Found at i:34064 original size:26 final size:28
Alignment explanation
Indices: 34003--34065 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
33993 CGAGTATTGC
*
34003 TGAGCTCGACTTGACTCGAAAACTCTGAAA
1 TGAGCTCGACTCGACTCGAAAACTCTG--A
34033 TGGAGCTCGACTCGACTCGAAAACTC-G-
1 T-GAGCTCGACTCGACTCGAAAACTCTGA
34060 TGAGCT
1 TGAGCT
34066 TAAAATTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 5 0.16
27 1 0.03
30 2 0.06
31 23 0.74
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (28 bp):
TGAGCTCGACTCGACTCGAAAACTCTGA
Found at i:36047 original size:29 final size:29
Alignment explanation
Indices: 36001--36062 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
35991 GTAGTAAACT
*
36001 ATAGTCGAGGGACCATTTTATAACTTTTA
1 ATAGGCGAGGGACCATTTTATAACTTTTA
* *
36030 ATAGGCGATGGACTATTTTATAACTTTTA
1 ATAGGCGAGGGACCATTTTATAACTTTTA
36059 ATAG
1 ATAG
36063 CCGGTGACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (29 bp):
ATAGGCGAGGGACCATTTTATAACTTTTA
Found at i:36107 original size:88 final size:89
Alignment explanation
Indices: 35955--36121 Score: 232
Period size: 88 Copynumber: 1.9 Consensus size: 89
35945 TCGAATGACC
* ** *
35955 ATTTTGTAACTTTTAATAGGTGAATGACTCAACAAAGTAGTAAACTATAGTCGAGGGACCATTTT
1 ATTTTATAACTTTTAATAGCCGAATGACTCAACAAAGCAGTAAACTATAGTCGAGGGACCATTTT
36020 ATAACTTTTAATAGGCGATGGACT
66 ATAACTTTTAATAGGCGATGGACT
* * *
36044 ATTTTATAACTTTTAATAGCCG-GTGACTCAACAAAGCA-TAATCCTATAGTCG-GGAGACTATT
1 ATTTTATAACTTTTAATAGCCGAATGACTCAACAAAGCAGTAA-ACTATAGTCGAGG-GACCATT
36106 TTATAACTTTTAATAG
64 TTATAACTTTTAATAG
36122 TCAAGAGACC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
87 5 0.07
88 45 0.65
89 19 0.28
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (89 bp):
ATTTTATAACTTTTAATAGCCGAATGACTCAACAAAGCAGTAAACTATAGTCGAGGGACCATTTT
ATAACTTTTAATAGGCGATGGACT
Found at i:39300 original size:31 final size:30
Alignment explanation
Indices: 39265--39358 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 30
39255 GAGTTAATTT
* *
39265 TTAATATGATTCTTAAAATTTAGATAAAATC
1 TTAATAT-AATCTTAAAATTTAGATAAAATA
* * * * *
39296 TTAATTTAACCCTGAAATTTTAAATAAAATA
1 TTAATATAA-TCTTAAAATTTAGATAAAATA
39327 TTAATATAATCATTAAAATTTAGATAAAATA
1 TTAATATAATC-TTAAAATTTAGATAAAATA
39358 T
1 T
39359 CAATTTAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
30 2 0.04
31 47 0.96
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (30 bp):
TTAATATAATCTTAAAATTTAGATAAAATA
Found at i:43846 original size:6 final size:6
Alignment explanation
Indices: 43835--43871 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
43825 TTAGAGGGAT
43835 GTTGGG GTTGGG GTTGGG GTTGGG GTTGGG GTTGGG G
1 GTTGGG GTTGGG GTTGGG GTTGGG GTTGGG GTTGGG G
43872 AAAGGGAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (6 bp):
GTTGGG
Found at i:44489 original size:26 final size:24
Alignment explanation
Indices: 44427--44489 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
44417 CATTTTAATC
44427 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
44451 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
44474 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
44490 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:44491 original size:22 final size:23
Alignment explanation
Indices: 44461--44507 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
44451 AAAATATATT
44461 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
44484 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
44506 TA
1 TA
44508 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:44521 original size:32 final size:32
Alignment explanation
Indices: 44455--44534 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
44445 ATATTTAAAA
* *
44455 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
44487 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
44519 TATATTATAATAATAT
1 TATATT-TATTAATAT
44535 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:44667 original size:27 final size:27
Alignment explanation
Indices: 44587--44678 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 27
44577 AGTAAAATTT
* *
44587 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
44614 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
44641 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
*
44670 ATAATATTT
1 ATATTATTT
44679 TAATAAAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
25 1 0.02
26 7 0.14
27 19 0.37
28 12 0.24
29 12 0.24
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:44698 original size:23 final size:23
Alignment explanation
Indices: 44679--44723 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
44669 AATAATATTT
44679 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
44702 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
44724 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:45101 original size:15 final size:15
Alignment explanation
Indices: 45068--45140 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 15
45058 TTCCAGAAAT
* *
45068 GTAATTCATTTTCCA
1 GTAATTCAATTTACA
45083 -TAATTCAATTTACA
1 GTAATTCAATTTACA
* *
45097 GTAATTCATTTTTCA
1 GTAATTCAATTTACA
*
45112 G-AATTCAATTTCCA
1 GTAATTCAATTTACA
* *
45126 GAAAATCAA-TTACA
1 GTAATTCAATTTACA
45140 G
1 G
45141 CCAAACAAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
14 29 0.60
15 19 0.40
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (15 bp):
GTAATTCAATTTACA
Found at i:45127 original size:14 final size:14
Alignment explanation
Indices: 45070--45128 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
45060 CCAGAAATGT
* *
45070 AATTCATTTTCCAT
1 AATTCAATTTCCAG
*
45084 AATTCAATTTACAG
1 AATTCAATTTCCAG
* *
45098 TAATTCATTTTTCAG
1 -AATTCAATTTCCAG
45113 AATTCAATTTCCAG
1 AATTCAATTTCCAG
45127 AA
1 AA
45129 AATCAATTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
14 25 0.68
15 12 0.32
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:46218 original size:2 final size:2
Alignment explanation
Indices: 46211--46242 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46201 GCATACGAAG
46211 AT AT 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 AT AT
46243 GGTTAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49172 original size:21 final size:21
Alignment explanation
Indices: 49129--49172 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
49119 GTGATTTTAG
* *
49129 TTTTTTTAATTTAATTAATAT
1 TTTTTTTAATTTAATCAACAT
*
49150 TTTTTTTATTTTAATCAACAT
1 TTTTTTTAATTTAATCAACAT
49171 TT
1 TT
49173 ATTAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTTTAATTTAATCAACAT
Found at i:52524 original size:18 final size:18
Alignment explanation
Indices: 52473--52524 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
52463 TTGTTGAAGG
*
52473 ATAACTTAAACAAA-TTA
1 ATAATTTAAACAAATTTA
* **
52490 ATAATTAAAACTTATTTA
1 ATAATTTAAACAAATTTA
52508 ATAATTTAAACAAATTT
1 ATAATTTAAACAAATTT
52525 TAACATTATA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATTTAAACAAATTTA
Found at i:54464 original size:14 final size:15
Alignment explanation
Indices: 54445--54473 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54435 CTGTTAATTG
54445 GAGTAAGAGG-AAAT
1 GAGTAAGAGGTAAAT
54459 GAGTAAGAGGTAAAT
1 GAGTAAGAGGTAAAT
54474 ACATTGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (15 bp):
GAGTAAGAGGTAAAT
Found at i:62830 original size:22 final size:21
Alignment explanation
Indices: 62788--62827 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62778 GAGTTTGTTT
*
62788 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
62809 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
62828 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:67624 original size:18 final size:19
Alignment explanation
Indices: 67597--67644 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
67587 GATGCAAGTA
*
67597 GTATCAATACTGA-GAGG-G
1 GTATCGATACT-ATGAGGAG
67615 GTATCGATACTATGAGGAAG
1 GTATCGATACTATGAGG-AG
67635 GTATCGATAC
1 GTATCGATAC
67645 CATTGATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 14 0.54
20 11 0.42
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (19 bp):
GTATCGATACTATGAGGAG
Found at i:67720 original size:22 final size:22
Alignment explanation
Indices: 67689--67764 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
67679 CGTAATAGAA
*
67689 TATCGGTACCATAATATAGTAG
1 TATCGATACCATAATATAGTAG
** **
67711 TATCGATACCAT--GGTAGGGG
1 TATCGATACCATAATATAGTAG
*
67731 TATCGATACCACAATATAGTAG
1 TATCGATACCATAATATAGTAG
67753 TATCGATACCAT
1 TATCGATACCAT
67765 GGTAGGGGTA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 15 0.37
22 26 0.63
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (22 bp):
TATCGATACCATAATATAGTAG
Found at i:67735 original size:20 final size:20
Alignment explanation
Indices: 67710--67781 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
67700 TAATATAGTA
67710 GTATCGATACCATGGTAGGG
1 GTATCGATACCATGGTAGGG
* **
67730 GTATCGATACCACAAT-ATAGTA
1 GTATCGATA-C-C-ATGGTAGGG
67752 GTATCGATACCATGGTAGGG
1 GTATCGATACCATGGTAGGG
*
67772 GTACCGATAC
1 GTATCGATAC
67782 TATTGAGACA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 22 0.54
21 2 0.05
22 13 0.32
23 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (20 bp):
GTATCGATACCATGGTAGGG
Found at i:67741 original size:42 final size:42
Alignment explanation
Indices: 67689--67781 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
67679 CGTAATAGAA
* *
67689 TATCGGTACCATAATATAGTAGTATCGATACCATGGTAGGGG
1 TATCGATACCACAATATAGTAGTATCGATACCATGGTAGGGG
67731 TATCGATACCACAATATAGTAGTATCGATACCATGGTAGGGG
1 TATCGATACCACAATATAGTAGTATCGATACCATGGTAGGGG
*
67773 TACCGATAC
1 TATCGATAC
67782 TATTGAGACA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (42 bp):
TATCGATACCACAATATAGTAGTATCGATACCATGGTAGGGG
Found at i:68189 original size:54 final size:54
Alignment explanation
Indices: 68098--68624 Score: 597
Period size: 54 Copynumber: 9.8 Consensus size: 54
68088 TACCAAATAG
* * *
68098 GCACTAAGTGTGTAAC-CACAGAATTCATCATATGTTGATGAGCAACCGTTTCA
1 GCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
* *
68151 GCACTAAGTGTGCAACTCACATAATTCATCATAAGTTGATTAACAACCGTTT-A
1 GCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
* * * *
68204 GACATTATGTGTGCAACCCAC-GAATTCATCATATGTTGATGAACAACCGTTTC-
1 G-CACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
* * *
68257 GACACTAAGTGTGCAACTCACATAATTCATCATAAGTTGATGAACAACTGTTTCG
1 G-CACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
* * ** * *
68312 GAACTAAGTGTGAAACTCATGGAATTCATCATAAGTTGATGAACAATC-ATTCA
1 GCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
* * **
68365 GGCACTAAATGTGCAACTCACGGAATTCATCATAAAATGATGAACAACC-TTTCA
1 -GCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
* * * *
68419 GGCACTAAGTTTGCAACTCATAGAATTCATCACAAGTTGATGAACAACC-ATTCA
1 -GCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
68473 GGCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCG-TTCA
1 -GCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
* * * * * *
68527 GGCACTATGTGTGCAACCCACAGAATTTATCATATGTTGATGATCAACCGTTTCG
1 -GCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
* * *
68582 GCACTATGTGTGCAAC-C-CATGAAATTCATAATAAGTTTATGAA
1 GCACTAAGTGTGCAACTCACA-G-AATTCATCATAAGTTGATGAA
68625 TTTCCGTATA
Statistics
Matches: 408, Mismatches: 56, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
52 2 0.00
53 68 0.17
54 334 0.82
55 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (54 bp):
GCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTTCA
Found at i:68458 original size:162 final size:160
Alignment explanation
Indices: 68097--68624 Score: 659
Period size: 162 Copynumber: 3.3 Consensus size: 160
68087 TTACCAAATA
* * * *
68097 GGCACTAAGTGTGTAAC-CACAGAATTCATCATATGTTGATGAGCAACCGTTTCAGCACTAAGTG
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAA-CGTTTCGGCACTAAGTG
* * * * *
68161 TGCAACTCACATAATTCATCATAAGTTGATTAACAACCGTTTAGACATTATGTGTGCAACCCACG
65 TGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTATGTGTGCAACCCACG
68226 AATTCATCATATGTTGATGAACAACCGTTTC
130 AATTCATCATATGTTGATGAACAACCGTTTC
* * *
68257 GACACTAAGTGTGCAACTCACATAATTCATCATAAGTTGATGAACAACTGTTTCGGAACTAAGTG
1 GGCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAAC-GTTTCGGCACTAAGTG
* ** * * ** *
68322 TGAAACTCATGGAATTCATCATAAGTTGATGAACAATCATTCAGGCACTAAATGTGCAACTCACG
65 TGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTATGTGTGCAACCCAC-
***
68387 GAATTCATCATAAAATGATGAACAACC-TTTC
129 GAATTCATCATATGTTGATGAACAACCGTTTC
* * * **
68418 AGGCACTAAGTTTGCAACTCATAGAATTCATCACAAGTTGATGAACAACCATTCAGGCACTAAGT
1 -GGCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACGTTTC-GGCACTAAGT
68483 GTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTATGTGTGCAACCCAC
64 GTGCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTATGTGTGCAACCCAC
* *
68548 AGAATTTATCATATGTTGATGATCAACCGTTTC
129 -GAATTCATCATATGTTGATGAACAACCGTTTC
* * *
68581 GGCACTATGTGTGCAAC-C-CATGAAATTCATAATAAGTTTATGAA
1 GGCACTAAGTGTGCAACTCACA-G-AATTCATCATAAGTTGATGAA
68625 TTTCCGTATA
Statistics
Matches: 309, Mismatches: 51, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
160 17 0.06
161 100 0.32
162 188 0.61
163 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (160 bp):
GGCACTAAGTGTGCAACTCACAGAATTCATCATAAGTTGATGAACAACGTTTCGGCACTAAGTGT
GCAACTCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGGCACTATGTGTGCAACCCACGA
ATTCATCATATGTTGATGAACAACCGTTTC
Found at i:68501 original size:29 final size:28
Alignment explanation
Indices: 68415--68501 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 28
68405 TGAACAACCT
*
68415 TTCAGGCACTAAGTTTGCAACTCATAGAA
1 TTCAGGCACTAAGTGTGCAACTCA-AGAA
* **
68444 TTCA-TCAC-AAGTTGATG-AA--CAACCA
1 TTCAGGCACTAAG-TG-TGCAACTCAAGAA
68469 TTCAGGCACTAAGTGTGCAACTCACAGAA
1 TTCAGGCACTAAGTGTGCAACTCA-AGAA
68498 TTCA
1 TTCA
68502 TCATAAGTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
25 8 0.19
26 9 0.21
27 6 0.14
28 8 0.19
29 12 0.28
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (28 bp):
TTCAGGCACTAAGTGTGCAACTCAAGAA
Found at i:68802 original size:45 final size:45
Alignment explanation
Indices: 68734--68916 Score: 258
Period size: 45 Copynumber: 4.1 Consensus size: 45
68724 CTAAAAGACT
* * *
68734 AAATGCATAAAGGTGCATTAAAGGCATGAAATGATGCCATTAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
* *
68779 AAATGCATAACGGTGTATCAAAGGCATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
* * * *
68824 AAATGTATAACGATGCATTAAAGGCATGAAAGGATTCCATTAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
* * *
68869 AAATACATAACGGTGCAGTAAAGGCATGAAAGGATGCCCTAAATG
1 AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
68914 AAA
1 AAA
68917 ATAATGAATA
Statistics
Matches: 120, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 120 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (45 bp):
AAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATG
Found at i:73611 original size:18 final size:17
Alignment explanation
Indices: 73573--73614 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
73563 ACCTTTTTCT
*
73573 CTCTTTTCTTGTTTATT
1 CTCTTTTCTTGTTTATC
73590 CTCTTCTTCTTGTTCT-TC
1 CTCTT-TTCTTGTT-TATC
73608 CTCTTTT
1 CTCTTTT
73615 TCCATCATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 14 0.64
19 1 0.05
ACGTcount: A:0.02, C:0.26, G:0.05, T:0.67
Consensus pattern (17 bp):
CTCTTTTCTTGTTTATC
Found at i:77438 original size:37 final size:37
Alignment explanation
Indices: 77345--77449 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
77335 TCTTTTTGTC
77345 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
77382 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * * *
77419 CTACTATTATTTAACCTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
77450 CCACAAACAT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:78013 original size:13 final size:13
Alignment explanation
Indices: 77995--78020 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
77985 TGTTTACTTA
77995 TTTACTATATTTT
1 TTTACTATATTTT
78008 TTTACTATATTTT
1 TTTACTATATTTT
78021 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:78036 original size:2 final size:2
Alignment explanation
Indices: 78029--78053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
78019 TTCCTAACGT
78029 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
78054 TCTTACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78224 original size:25 final size:28
Alignment explanation
Indices: 78178--78237 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 28
78168 TATACATACA
78178 TTTTTA-TATTTATATATATATA-TATAT
1 TTTTTATTATTTATATATATATACTAT-T
78205 TTTTTATTATTT-TAT-T-TATACTATT
1 TTTTTATTATTTATATATATATACTATT
*
78230 TATTTATT
1 TTTTTATT
78238 TTCATTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 12 0.40
26 4 0.13
27 9 0.30
28 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTTTATTATTTATATATATATACTATT
Found at i:78360 original size:15 final size:15
Alignment explanation
Indices: 78342--78371 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
78332 ATCTTCATTT
78342 ATTTTATTTTATTCA
1 ATTTTATTTTATTCA
*
78357 ATTTTATTTTTTTCA
1 ATTTTATTTTATTCA
78372 TCCAATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATTTTATTCA
Found at i:78377 original size:19 final size:20
Alignment explanation
Indices: 78339--78378 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
78329 TTTATCTTCA
* *
78339 TTTATTTTATTTTATTCAAT
1 TTTATTTTATTTCATCCAAT
78359 TTTATTTT-TTTCATCCAAT
1 TTTATTTTATTTCATCCAAT
78378 T
1 T
78379 ATTTTATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTTTATTTCATCCAAT
Found at i:80375 original size:29 final size:30
Alignment explanation
Indices: 80304--80376 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
80294 AAAATTACCC
* *
80304 TTTTGGTCCCTAAACTTTTTTAAACTTTGTA
1 TTTTGGTCACTAAAC-TTTTTAAACTTTATA
* * * *
80335 CTTTCGTAACTAAAC-TTTTAAATTTTATA
1 TTTTGGTCACTAAACTTTTTAAACTTTATA
80364 TTTTGGTCACTAA
1 TTTTGGTCACTAA
80377 CCAAAGTTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
29 22 0.67
31 11 0.33
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.49
Consensus pattern (30 bp):
TTTTGGTCACTAAACTTTTTAAACTTTATA
Found at i:88683 original size:3 final size:3
Alignment explanation
Indices: 88659--88713 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
88649 TAAACACACT
* * * *
88659 TAA TAA TAC TAA TAC TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
88706 TAA TAA TA
1 TAA TAA TA
88714 TTTTTTAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:89775 original size:28 final size:28
Alignment explanation
Indices: 89743--89799 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
89733 TTACTAACAT
89743 AGGCATACAATAGAAAATAAATTCCTAA
1 AGGCATACAATAGAAAATAAATTCCTAA
89771 AGGCATACAATAGAAAATAAATTCCTAA
1 AGGCATACAATAGAAAATAAATTCCTAA
89799 A
1 A
89800 AAAAATTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (28 bp):
AGGCATACAATAGAAAATAAATTCCTAA
Found at i:91273 original size:29 final size:29
Alignment explanation
Indices: 91226--91281 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
91216 CCTTAAATTT
*
91226 TTTCAAATTTTATACTTT-GTCTACTAAAC
1 TTTCAAAATTTATACTTTGGTC-ACTAAAC
**
91255 TTTCAAAATTTATGTTTTGGTCACTAA
1 TTTCAAAATTTATACTTTGGTCACTAA
91282 CTAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.48
Consensus pattern (29 bp):
TTTCAAAATTTATACTTTGGTCACTAAAC
Found at i:92106 original size:27 final size:27
Alignment explanation
Indices: 92073--92129 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
92063 CCTCCTTAAA
92073 ATTAACGATCTTTATGAAACCACTTAC
1 ATTAACGATCTTTATGAAACCACTTAC
92100 ATTAACGATCTTTATGAAACCACTTAC
1 ATTAACGATCTTTATGAAACCACTTAC
92127 ATT
1 ATT
92130 CCCCACATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (27 bp):
ATTAACGATCTTTATGAAACCACTTAC
Found at i:98395 original size:16 final size:16
Alignment explanation
Indices: 98371--98404 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
98361 TATCGCCGAC
*
98371 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
98387 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
98403 CG
1 CG
98405 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:101944 original size:20 final size:20
Alignment explanation
Indices: 101919--101964 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
101909 ACACAATGAC
101919 AAATAAACATCATAACTAAA
1 AAATAAACATCATAACTAAA
*
101939 AAATAAACATGATAACTAAA
1 AAATAAACATCATAACTAAA
101959 AGAATA
1 A-AATA
101965 GGGAGAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.65, C:0.11, G:0.04, T:0.20
Consensus pattern (20 bp):
AAATAAACATCATAACTAAA
Found at i:102822 original size:11 final size:11
Alignment explanation
Indices: 102806--102830 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
102796 GCTGTGCGGC
102806 GGTTAAAAAAT
1 GGTTAAAAAAT
102817 GGTTAAAAAAT
1 GGTTAAAAAAT
102828 GGT
1 GGT
102831 GTGACCGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (11 bp):
GGTTAAAAAAT
Found at i:102966 original size:23 final size:23
Alignment explanation
Indices: 102922--102966 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
102912 AACAAATTAT
**
102922 GTAGCGCTTATATAATGTAATAG
1 GTAGCGCTTATATAATAAAATAG
102945 GTAGCGCTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
102967 TGTTAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAG
Found at i:103023 original size:23 final size:23
Alignment explanation
Indices: 102997--103056 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
102987 ATCAAGCACA
* *
102997 ATAACATATTAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
103020 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
103043 ATAATAAAATAGGT
1 ATAACATAATAGGT
103057 TAATTACTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:103034 original size:87 final size:87
Alignment explanation
Indices: 102888--103131 Score: 407
Period size: 87 Copynumber: 2.8 Consensus size: 87
102878 ATATCATTTA
* * *
102888 ACTGGAAATATTATCAAGTAAAATAACAAATTATGTAGCGCTTATATAATGTAATAGGTAGCGCT
1 ACTGGAAATATTATCAAGTACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGTAGCGCT
*
102953 TATATAATAAAATATGTTAATT
66 TATATAATAAAATAGGTTAATT
* * * *
102975 ACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGTTTATATAATGTAATAGGTAGCGCT
1 ACTGGAAATATTATCAAGTACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGTAGCGCT
103040 TATATAATAAAATAGGTTAATT
66 TATATAATAAAATAGGTTAATT
*
103062 ACTAGAAATATTATCAAGTACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGTAGCGCT
1 ACTGGAAATATTATCAAGTACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGTAGCGCT
103127 TATAT
66 TATAT
103132 TGACCTATTC
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 145 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
ACTGGAAATATTATCAAGTACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGTAGCGCT
TATATAATAAAATAGGTTAATT
Found at i:103732 original size:200 final size:199
Alignment explanation
Indices: 103242--103762 Score: 794
Period size: 198 Copynumber: 2.6 Consensus size: 199
103232 AATTTTAAAT
* * *
103242 GTATCGACACAAACTTAAAATGTGTCGATACATTATGTATACATATTTTCTCATAAAACCGGTAT
1 GTATCGACACAAACTTAAAATGTGTCGATACATTATGTAAACCTATTTTCTCATAAAACCGATAT
* * * *
103307 ATTTCTACCGGGTACATTGTAAATTTACCTATTACATTGTAATTATCAGTTTGGAT-TTTTTGGG
66 ATTTCTACTGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGG
*
103371 ATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTCATTAGACATTCATTCTGGAA
131 ATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTAGACATTCATTCTGGAA
103436 AAAA
196 AAAA
103440 GTATCGACACAAACTTAAAATGTGTCGATACATTATGTAAACCTATTTTCTCATAAAACCGATAT
1 GTATCGACACAAACTTAAAATGTGTCGATACATTATGTAAACCTATTTTCTCATAAAACCGATAT
*
103505 ATTTCTACTGATTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGG
66 ATTTCTACTGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGG
* * *
103570 ATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTCTGGGG
131 ATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTAGACATTCATTCT-GGA
*
103635 AAAAT
195 AAAAA
*** * * * * *
103640 GTATCGACAC-TTTTTAAATTTGTGTTGATACATTATGTAGACCTATTCTCTCATAAAACTGATA
1 GTATCGACACAAACTTAAA-ATGTGTCGATACATTATGTAAACCTATTTTCTCATAAAACCGATA
* * *
103704 TATTTATACTGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
65 TATTTCTACTGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGT
103763 AACATATGTG
Statistics
Matches: 295, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
198 113 0.38
199 71 0.24
200 111 0.38
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (199 bp):
GTATCGACACAAACTTAAAATGTGTCGATACATTATGTAAACCTATTTTCTCATAAAACCGATAT
ATTTCTACTGGTTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGG
ATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTAGACATTCATTCTGGAA
AAAA
Found at i:103956 original size:14 final size:14
Alignment explanation
Indices: 103888--103960 Score: 53
Period size: 14 Copynumber: 5.3 Consensus size: 14
103878 ATAACAATTT
103888 TATTTTAATAA-AA
1 TATTTTAATAATAA
** *
103901 TATAATAATCATAA
1 TATTTTAATAATAA
*
103915 T-TTTTAATTTATAA
1 TATTTTAA-TAATAA
* *
103929 AATTATAGAT-ATAA
1 TATTTTA-ATAATAA
103943 TATTTTAATAATAA
1 TATTTTAATAATAA
103957 TATT
1 TATT
103961 GACATAAATA
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
13 14 0.31
14 25 0.56
15 5 0.11
16 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:103956 original size:28 final size:28
Alignment explanation
Indices: 103888--103956 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
103878 ATAACAATTT
*
103888 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* *
103915 T-TTTTAATTTATAAAATTATAGAT-ATAA
1 TATTTTAA-TAATAAAATAATA-ATCATAA
103943 TATTTTAATAATAA
1 TATTTTAATAATAA
103957 TATTGACATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
26 6 0.18
27 3 0.09
28 17 0.50
29 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:104676 original size:31 final size:30
Alignment explanation
Indices: 104639--104729 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
104629 TAAAAAATAA
*
104639 AAAATATAATTTATAATAATTTTATT-TTAAT
1 AAAATATAA-TAATAATAATTTT-TTATTAAT
* *
104670 AAAATATAATAATCATAATTTTTTATTTAT
1 AAAATATAATAATAATAATTTTTTATTAAT
* *
104700 AAAAT-T-ATAGAT-ATAATATTTTAATAAT
1 AAAATATAATA-ATAATAATTTTTTATTAAT
104728 AA
1 AA
104730 TATTTACATA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
28 18 0.35
29 5 0.10
30 20 0.38
31 9 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
AAAATATAATAATAATAATTTTTTATTAAT
Found at i:104729 original size:14 final size:14
Alignment explanation
Indices: 104647--104748 Score: 57
Period size: 14 Copynumber: 7.2 Consensus size: 14
104637 AAAAAATATA
**
104647 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
104662 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
104675 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
104689 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
104703 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
104717 ATTTTAATAATAAT
1 ATTTTAATAATAAT
104731 A-TTTACATAAATAAT
1 ATTTTA-AT-AATAAT
104746 ATT
1 ATT
104749 AAATAAATTA
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
13 14 0.22
14 38 0.58
15 12 0.18
16 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:104729 original size:28 final size:28
Alignment explanation
Indices: 104661--104729 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
104651 ATAATAATTT
*
104661 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
104688 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
104716 TATTTTAATAATAA
1 TATTTTAATAATAA
104730 TATTTACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:104754 original size:14 final size:15
Alignment explanation
Indices: 104712--104756 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
104702 AATTATAGAT
*
104712 ATAATATTTTAAT-A
1 ATAATATTTAAATAA
*
104726 ATAATATTTACATAA
1 ATAATATTTAAATAA
104741 ATAATA-TTAAATAA
1 ATAATATTTAAATAA
104755 AT
1 AT
104757 TATTCTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATATTTAAATAA
Found at i:104816 original size:24 final size:24
Alignment explanation
Indices: 104765--104816 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
104755 ATTATTCTAA
104765 TATT-TTAAAAATAATATTATTAT
1 TATTGTTAAAAATAATATTATTAT
*
104788 T-TTGTTAATAAATAATATTGTT-T
1 TATTGTTAA-AAATAATATTATTAT
104811 TATTGT
1 TATTGT
104817 ATTTGATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 7 0.28
24 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (24 bp):
TATTGTTAAAAATAATATTATTAT
Found at i:105202 original size:87 final size:87
Alignment explanation
Indices: 105054--105248 Score: 336
Period size: 87 Copynumber: 2.2 Consensus size: 87
105044 AAAAATTAAA
* * *
105054 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTTATATGTTA
1 TAATTAACCTATTTTATTATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTA
105119 TTGTGCTTGATAATGTTTCCAG
66 TTGTGCTTGATAATGTTTCCAG
* *
105141 TAATTAACCTATTTTATTATATAAGCACTACTTATTACATTATATAAGCGGTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTA
*
105206 TTGTGCTTGATAATGTTTTCAG
66 TTGTGCTTGATAATGTTTCCAG
105228 TAATTAACCTATTTTATTATA
1 TAATTAACCTATTTTATTATA
105249 CCTATTACAT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 102 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (87 bp):
TAATTAACCTATTTTATTATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTA
TTGTGCTTGATAATGTTTCCAG
Found at i:105281 original size:23 final size:23
Alignment explanation
Indices: 105247--105332 Score: 145
Period size: 23 Copynumber: 3.7 Consensus size: 23
105237 TATTTTATTA
*
105247 TACCTATTACATTATATAAGCAC
1 TACCTATTACATTATATAAGCGC
*
105270 TACATATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
105293 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
*
105316 TACCTATTACATCATAT
1 TACCTATTACATTATAT
105333 TTTTACCTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGC
Found at i:107190 original size:29 final size:29
Alignment explanation
Indices: 107162--107267 Score: 131
Period size: 29 Copynumber: 3.6 Consensus size: 29
107152 ATAAAATATT
* * * *
107162 TTAACCTATAAATGTATTTTATTTTTATT
1 TTAACTTAAAAATATATTTTATTTTTATC
* *
107191 TTAACTTAAAAATATATTTTAATCTTATC
1 TTAACTTAAAAATATATTTTATTTTTATC
*
107220 TTAACTTAAAAATATATTTTGTTTTTATC
1 TTAACTTAAAAATATATTTTATTTTTATC
107249 TTAACTTTTAAAAATATAT
1 TTAAC--TTAAAAATATAT
107268 CTTTCTTAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
29 54 0.82
31 12 0.18
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.53
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTTTTATC
Found at i:108978 original size:29 final size:26
Alignment explanation
Indices: 108934--109027 Score: 100
Period size: 29 Copynumber: 3.3 Consensus size: 26
108924 ATTTTAACCT
*
108934 AAAA-ATATTTTTTTATTTTAACTTA
1 AAAATATATTTTTTTATCTTAACTTA
108959 AAAATATATTTTAATCTTATCTTAACTTA
1 AAAATATATTTT--T-TTATCTTAACTTA
108988 AAAATATATTTTGTTTTTATCTTAACTTTTA
1 AAAATATA--TT-TTTTTATCTTAAC--TTA
109019 AAAATATAT
1 AAAATATAT
109028 CTTTCTTAGT
Statistics
Matches: 59, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
25 4 0.07
26 7 0.12
28 1 0.02
29 31 0.53
30 1 0.02
31 13 0.22
32 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.52
Consensus pattern (26 bp):
AAAATATATTTTTTTATCTTAACTTA
Found at i:109011 original size:24 final size:24
Alignment explanation
Indices: 108925--109012 Score: 79
Period size: 24 Copynumber: 3.5 Consensus size: 24
108915 TTGAATAATA
* *
108925 TTTTAACCTAAAAATAT-TTTTTT
1 TTTTAACTTAAAAATATATTTTCT
108948 ATTTTAACTTAAAAATATATTTTAATCT
1 -TTTTAACTTAAAAATATA-TTT--TCT
*
108976 TATCTTAACTTAAAAATATATTTTGT
1 T-T-TTAACTTAAAAATATATTTTCT
*
109002 TTTTATCTTAA
1 TTTTAACTTAA
109013 CTTTTAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
24 24 0.44
25 1 0.02
26 6 0.11
27 1 0.02
28 6 0.11
29 16 0.30
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (24 bp):
TTTTAACTTAAAAATATATTTTCT
Found at i:109999 original size:27 final size:27
Alignment explanation
Indices: 109961--110014 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
109951 AGTTGAAAGG
109961 TACTCATATGATTGTTTGAGTGAGTTT
1 TACTCATATGATTGTTTGAGTGAGTTT
109988 TACTCATATGATTGTTTGAGTGAGTTT
1 TACTCATATGATTGTTTGAGTGAGTTT
110015 GATATTGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (27 bp):
TACTCATATGATTGTTTGAGTGAGTTT
Found at i:118805 original size:3 final size:3
Alignment explanation
Indices: 118797--118849 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
118787 GGTAAATATA
*
118797 ATT ATT ATT A-A ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
118844 ATT ATT
1 ATT ATT
118850 TATATTTTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 1 0.02
3 46 0.98
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:120607 original size:33 final size:33
Alignment explanation
Indices: 120570--120639 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 33
120560 AAACATATAT
* *
120570 TTTTGTTTATTTATTTTATTTATGT-TATT-AATG
1 TTTTG-TTA-TTATATTATATATGTATATTGAATG
120603 TTTTGTTATTATATTATATATGTAATATTGAATG
1 TTTTGTTATTATATTATATATGT-ATATTGAATG
120637 TTT
1 TTT
120640 GTCTAATGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 13 0.41
32 3 0.09
33 9 0.28
34 7 0.22
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (33 bp):
TTTTGTTATTATATTATATATGTATATTGAATG
Found at i:125411 original size:4 final size:4
Alignment explanation
Indices: 125402--127066 Score: 2991
Period size: 4 Copynumber: 421.8 Consensus size: 4
125392 TTTATCCATA
125402 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125450 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125498 TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG TA-G
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125544 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125592 TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125638 TATG TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
125685 TATG TATG TATG TATA TGTA TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125733 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125780 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125828 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125876 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125924 TATG TATG TA-G -ATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
125970 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TTATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG -TATG
126019 TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126065 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
126113 TAGG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126161 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126209 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126257 TATG TATG TA-- TATG TATG TA-G TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126302 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126350 TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126397 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126445 TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
126491 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TGTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126539 TATG TA-G TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126584 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126632 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126680 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126727 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126775 TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
126821 TATG TCTG TATG TATG TCATG TATG TATG CATG CATG -ATG CATG CATG
1 TATG TATG TATG TATG T-ATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * *
126869 CATG CATG CATG CA-G CATG CATG TATG CATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126916 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
126964 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
127012 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
127060 TATG TAT
1 TATG TAT
127067 ATCCCTTGTT
Statistics
Matches: 1621, Mismatches: 14, Indels: 52
0.96 0.01 0.03
Matches are distributed among these distances:
2 13 0.01
3 32 0.02
4 1568 0.97
5 8 0.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:129940 original size:17 final size:17
Alignment explanation
Indices: 129909--129978 Score: 56
Period size: 17 Copynumber: 4.0 Consensus size: 17
129899 ATATTACACT
129909 TAAAAAAGAGCAAAAAGA
1 TAAAAAAGAGCAAAAA-A
*
129927 TAAAAAAGA-TAAAAAA
1 TAAAAAAGAGCAAAAAA
129943 TAGAAAAAGAAG-AAGAAAA
1 TA-AAAAAG-AGCAA-AAAA
*
129962 -AGAAAAGAAGCAAAAAA
1 TAAAAAAG-AGCAAAAAA
129979 AGGAAAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.07
17 23 0.51
18 15 0.33
19 4 0.09
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.06
Consensus pattern (17 bp):
TAAAAAAGAGCAAAAAA
Found at i:129949 original size:9 final size:8
Alignment explanation
Indices: 129910--129987 Score: 57
Period size: 9 Copynumber: 8.6 Consensus size: 8
129900 TATTACACTT
129910 AAAAAAGA
1 AAAAAAGA
*
129918 GCAAAAAGA
1 -AAAAAAGA
129927 TAAAAAAGATA
1 -AAAAAAG--A
129938 AAAAATAGA
1 AAAAA-AGA
129947 AAAAGAAGA
1 AAAA-AAGA
129956 AGAAAAAGA
1 A-AAAAAGA
*
129965 AAAGAAGCA
1 AAAAAAG-A
129974 AAAAAAGGA
1 AAAAAA-GA
129983 AAAAA
1 AAAAA
129988 TAAAGGAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.09
9 39 0.68
10 10 0.18
11 3 0.05
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:129965 original size:18 final size:17
Alignment explanation
Indices: 129929--129986 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
129919 CAAAAAGATA
*
129929 AAAAAGATA-AAAAATAG
1 AAAAAGA-AGAAAAAAAG
129946 AAAAAGAAGAAGAAAAAG
1 AAAAAGAAGAA-AAAAAG
129964 -AAAAGAAGCAAAAAAAGG
1 AAAAAGAAG-AAAAAAA-G
129982 AAAAA
1 AAAAA
129987 ATAAAGGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 1 0.03
17 22 0.63
18 8 0.23
19 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAAAGAAGAAAAAAAG
Found at i:131760 original size:40 final size:42
Alignment explanation
Indices: 131668--131767 Score: 107
Period size: 46 Copynumber: 2.3 Consensus size: 42
131658 ACTAGTTGTA
* *
131668 CTCATCTCGTAGGAACCGTGTTATCACCCTTAGATGGCCTGACATC
1 CTCATCACGTAGGAACCGTGTCATCACCC-T-GA--GCCTGACATC
131714 CTCATCACGTAGGAACCGTGTCATCACCC-GA-CCTGATC-TC
1 CTCATCACGTAGGAACCGTGTCATCACCCTGAGCCTGA-CATC
*
131754 CTCATCAAGTAGGA
1 CTCATCACGTAGGA
131768 GCTGCGTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
40 20 0.40
41 1 0.02
43 2 0.04
46 27 0.54
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (42 bp):
CTCATCACGTAGGAACCGTGTCATCACCCTGAGCCTGACATC
Found at i:131924 original size:52 final size:52
Alignment explanation
Indices: 131790--131915 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
131780 CGTGATAACC
* * *
131790 AGAACTCTTCATCACATATGAGTCGTGTTATCACCCTTTCTAAATATGGTTA
1 AGAACTCTTCATCACATATGAGTCGTGTTATCACCCTTCCTAAATACGGTCA
131842 AGAACTCTTCATCACATATGAGTCGTGTTATCACCCTTCCTAAATACGGTCA
1 AGAACTCTTCATCACATATGAGTCGTGTTATCACCCTTCCTAAATACGGTCA
*
131894 AGAACTCTTCATCACGTATGAG
1 AGAACTCTTCATCACATATGAG
131916 CAGAGTTATA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (52 bp):
AGAACTCTTCATCACATATGAGTCGTGTTATCACCCTTCCTAAATACGGTCA
Found at i:132167 original size:3 final size:3
Alignment explanation
Indices: 132152--132193 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
132142 TCTATATAAA
* *
132152 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
132194 TTACATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:146161 original size:8 final size:8
Alignment explanation
Indices: 146148--146175 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
146138 GGATTCTCCC
146148 ATATGTAT
1 ATATGTAT
146156 ATATGTAT
1 ATATGTAT
146164 ATATGTAT
1 ATATGTAT
146172 ATAT
1 ATAT
146176 CTTCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:149690 original size:8 final size:8
Alignment explanation
Indices: 149673--149724 Score: 70
Period size: 8 Copynumber: 6.5 Consensus size: 8
149663 GAAATGAGTG
*
149673 AAAATGAA
1 AAAATAAA
149681 AAAATAAA
1 AAAATAAA
149689 AAAATAAA
1 AAAATAAA
149697 AAAAT-AA
1 AAAATAAA
*
149704 AAAATGAA
1 AAAATAAA
149712 AAAATGAAA
1 AAAAT-AAA
149721 AAAA
1 AAAA
149725 GAAGGGTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.17
8 27 0.68
9 6 0.15
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:149698 original size:16 final size:16
Alignment explanation
Indices: 149673--149724 Score: 79
Period size: 15 Copynumber: 3.2 Consensus size: 16
149663 GAAATGAGTG
149673 AAAATGAAAAAATAAA
1 AAAATGAAAAAATAAA
*
149689 AAAATAAAAAAAT-AA
1 AAAATGAAAAAATAAA
149704 AAAATGAAAAAATGAAA
1 AAAATGAAAAAAT-AAA
149721 AAAA
1 AAAA
149725 GAAGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 14 0.44
16 12 0.38
17 6 0.19
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAATGAAAAAATAAA
Found at i:150716 original size:55 final size:55
Alignment explanation
Indices: 150650--151147 Score: 829
Period size: 55 Copynumber: 9.1 Consensus size: 55
150640 TTTCCCAACA
150650 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
1 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
* * *
150705 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTTAAGAAATAGGGAGCAAACACA
1 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
* *
150760 ATTGTTGAAGATTATTCGAGTCTCATACTCTTTGAAGAAATAGGGAGCAGACACG
1 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
* *
150815 ATTGTTAAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACA
1 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
150870 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
1 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
150925 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
1 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
* * *
150980 ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAACAAATAGGGAACAGACACG
1 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
* *
151035 ATTGTTAAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGCACG
1 ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
* * * *
151090 ATTATCG-AGAATCGTTCGAGTCTTATACTCTCTGAA-AAATAGGGAGCAGACACG
1 ATTGTTGAAG-ATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
151144 ATTG
1 ATTG
151148 ACGAAGATAT
Statistics
Matches: 413, Mismatches: 29, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
54 22 0.05
55 391 0.95
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (55 bp):
ATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG
Found at i:167390 original size:18 final size:18
Alignment explanation
Indices: 167367--167404 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
167357 GCCAGCTCGG
167367 ACAGAACCCCTCCAAGAT
1 ACAGAACCCCTCCAAGAT
167385 ACAGAACCCCTCCAAGAT
1 ACAGAACCCCTCCAAGAT
167403 AC
1 AC
167405 GGATGGCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.39, G:0.11, T:0.11
Consensus pattern (18 bp):
ACAGAACCCCTCCAAGAT
Done.