Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000263.1 Hibiscus syriacus cultivar Beakdansim tig00000485_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: 51557
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:161 original size:19 final size:20
Alignment explanation
Indices: 132--182 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
122 AACGCGATCC
132 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
152 CCAG-ATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
171 CCAAAATCGCAA
1 CCAGAATCGCAA
183 CGCGATTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:260 original size:20 final size:20
Alignment explanation
Indices: 237--327 Score: 64
Period size: 20 Copynumber: 4.6 Consensus size: 20
227 CGATTTCCAT
* *
237 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
257 AATCGC-ACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
276 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
296 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
316 AATCGCAACGCG
1 AATCGCAACGCG
328 TATGGGTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.02
19 15 0.24
20 44 0.71
21 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:330 original size:20 final size:20
Alignment explanation
Indices: 274--425 Score: 204
Period size: 20 Copynumber: 7.7 Consensus size: 20
264 CGCGAACACA
274 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
294 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
314 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
334 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
354 T--ATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
372 TAAATCGCAA--CGTAATACA
1 TAAATCGCAACGCGT-ATCCG
391 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
412 TAAATCGCAACGCG
1 TAAATCGCAACGCG
426 ATATTAAAGC
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
18 20 0.18
19 4 0.04
20 83 0.73
21 4 0.04
22 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:379 original size:78 final size:78
Alignment explanation
Indices: 277--421 Score: 229
Period size: 78 Copynumber: 1.9 Consensus size: 78
267 GAACACATAA
* * * **
277 ATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT-AAATCGCAACGCGTATGGGTAAATCG
1 ATCGCAACGCGTATCCGTAAATCGCAACGT-AATACATAAAATCGCAACGCGTATCCGTAAATCG
341 CAATGCGTATCCGT
65 CAATGCGTATCCGT
355 ATCGCAACGCGTATCCGTAAATCGCAACGTAATACATAAAATCGCAACGCGTATCCGTAAATCGC
1 ATCGCAACGCGTATCCGTAAATCGCAACGTAATACATAAAATCGCAACGCGTATCCGTAAATCGC
420 AA
66 AA
422 CGCGATATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 4 0.07
78 57 0.93
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (78 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGTAATACATAAAATCGCAACGCGTATCCGTAAATCGC
AATGCGTATCCGT
Found at i:839 original size:32 final size:32
Alignment explanation
Indices: 798--863 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
788 TTCACTTAGA
*
798 TTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
830 TTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTCATTTCGCGTTACGATTCTCTCGTTGCGAT
862 TT
1 TT
864 TCAGTTAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.47
Consensus pattern (32 bp):
TTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:967 original size:20 final size:20
Alignment explanation
Indices: 942--996 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
932 TGCAGAAGAG
*
942 TCGCAACGAGATAATGAAAA
1 TCGCAACGAGAGAATGAAAA
***
962 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
982 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
997 CGCAAACGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1048 original size:32 final size:34
Alignment explanation
Indices: 982--1052 Score: 110
Period size: 32 Copynumber: 2.1 Consensus size: 34
972 AGAATGACTG
**
982 TCGCAACGAGAGAATCGCAAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAAACGCGAAACCAAAA
1016 TCGCAACGA-AGAATCGC-AACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAAACGCGAAACCAAAA
1048 TCGCA
1 TCGCA
1053 TTGCGATTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 18 0.51
33 8 0.23
34 9 0.26
ACGTcount: A:0.45, C:0.25, G:0.21, T:0.08
Consensus pattern (34 bp):
TCGCAACGAGAGAATCGCAAACGCGAAACCAAAA
Found at i:1086 original size:19 final size:19
Alignment explanation
Indices: 1058--1148 Score: 83
Period size: 19 Copynumber: 5.3 Consensus size: 19
1048 TCGCATTGCG
1058 ATTTCTCGTTGCGATTTTC
1 ATTTCTCGTTGCGATTTTC
*
1077 ATTTCGCGTTGCGA--TTC
1 ATTTCTCGTTGCGATTTTC
*
1094 ---TCTCGTTGCGATTGTC
1 ATTTCTCGTTGCGATTTTC
* *
1110 ATCTCGCGTTGCGA-TTTC
1 ATTTCTCGTTGCGATTTTC
1128 ---TCTCGTTGCGATTTTC
1 ATTTCTCGTTGCGATTTTC
1144 ATTTC
1 ATTTC
1149 AACCAAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
14 10 0.18
15 10 0.18
16 6 0.11
17 3 0.05
18 3 0.05
19 25 0.44
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (19 bp):
ATTTCTCGTTGCGATTTTC
Found at i:1101 original size:33 final size:33
Alignment explanation
Indices: 1048--1148 Score: 159
Period size: 33 Copynumber: 3.1 Consensus size: 33
1038 GAAACCAAAA
*
1048 TCGCATTGCGATT-TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
* *
1080 TCGCGTTGCGATTCTCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1113 TCGCGTTGCGATTTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTCTCTCGTTGCGATTTTCATT
1147 TC
1 TC
1149 AACCAAAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.19
33 28 0.45
34 22 0.35
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:3110 original size:93 final size:93
Alignment explanation
Indices: 2823--3291 Score: 885
Period size: 91 Copynumber: 5.1 Consensus size: 93
2813 TAGATTGCTT
*
2823 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2888 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2916 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTG-AATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2978 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3006 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3071 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3099 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3162 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3190 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3255 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3283 AGTAAATTT
1 AGTAAATTT
3292 ATCCATTCAA
Statistics
Matches: 368, Mismatches: 3, Indels: 10
0.97 0.01 0.03
Matches are distributed among these distances:
90 36 0.10
91 143 0.39
92 54 0.15
93 135 0.37
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3198 original size:184 final size:184
Alignment explanation
Indices: 2823--3291 Score: 904
Period size: 184 Copynumber: 2.6 Consensus size: 184
2813 TAGATTGCTT
*
2823 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2888 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
2952 GTATATTCTTTAACACTGTGAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3006 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3071 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
3136 GTGTATTCTTTAACACTGTGAAAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3190 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3255 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
3292 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
183 98 0.35
184 184 0.65
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (184 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAAATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3375 original size:19 final size:19
Alignment explanation
Indices: 3335--3463 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3325 TAGTTTACTT
* *
3335 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3355 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3374 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3393 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3407 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3426 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3440 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3459 TCGCA
1 TCGCA
3464 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3414 original size:33 final size:32
Alignment explanation
Indices: 3371--3463 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
3361 CGCGAAACCA
**
3371 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3403 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
3436 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3464 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:3461 original size:52 final size:52
Alignment explanation
Indices: 3335--3463 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
3325 TAGTTTACTT
**
3335 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
3387 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
3440 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
3464 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:3481 original size:19 final size:19
Alignment explanation
Indices: 3459--3593 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3449 GAAACCAAAA
*
3459 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3478 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3494 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3511 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3527 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3544 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3563 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3583 TCGTGTTGCGA
1 TCGCGTTGCGA
3594 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3500 original size:14 final size:14
Alignment explanation
Indices: 3481--3537 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3471 TTTCATTTCG
3481 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3495 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3512 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3528 CGTTGCGATT
1 CGTTGCGATT
3538 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3506 original size:33 final size:33
Alignment explanation
Indices: 3464--3556 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3454 CAAAATCGCA
*
3464 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
3497 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3530 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3557 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:5508 original size:14 final size:14
Alignment explanation
Indices: 5489--5524 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5479 ATTGTTTAAT
5489 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5503 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5517 TGATTTGT
1 TGATTTGT
5525 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:5717 original size:20 final size:19
Alignment explanation
Indices: 5631--5731 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
5621 AAAAATGACT
5631 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5650 ATCGCAATGCG-AATGAAA
1 ATCGCAATGCGAAATGAAA
*
5668 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5682 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5701 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
5721 ATCGCAATGCG
1 ATCGCAATGCG
5732 TTATAATTTC
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 4 0.05
18 15 0.20
19 25 0.34
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5783 original size:19 final size:19
Alignment explanation
Indices: 5759--6051 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
5749 GATTATCTCG
5759 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5778 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5797 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
5811 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5830 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5849 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5868 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5887 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5906 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5925 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
5939 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5958 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5977 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5991 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
6011 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
6025 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
6044 TTGCGATT
1 TTGCGATT
6052 GTATTTTCCG
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 29 0.12
16 24 0.10
17 20 0.08
18 3 0.01
19 157 0.64
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5798 original size:52 final size:52
Alignment explanation
Indices: 5737--6051 Score: 330
Period size: 52 Copynumber: 5.9 Consensus size: 52
5727 ATGCGTTATA
*
5737 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
5789 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
5841 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
5898 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
5950 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
6002 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
6052 GTATTTTCCG
Statistics
Matches: 241, Mismatches: 9, Indels: 25
0.88 0.03 0.09
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 4 0.02
52 129 0.54
53 18 0.07
54 6 0.02
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:5921 original size:128 final size:122
Alignment explanation
Indices: 5759--6023 Score: 194
Period size: 128 Copynumber: 2.1 Consensus size: 122
5749 GATTATCTCG
*
5759 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
5821 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
5885 CA
121 CA
* * *
5887 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
5949 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
6009 CA
121 CA
6011 TTGCGATTTTCAT
1 TTGCGATTTTCAT
6024 GTTGGGATTT
Statistics
Matches: 125, Mismatches: 5, Indels: 18
0.84 0.03 0.12
Matches are distributed among these distances:
121 7 0.06
122 4 0.03
123 18 0.14
124 18 0.14
125 2 0.02
126 2 0.02
128 74 0.59
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:8343 original size:12 final size:12
Alignment explanation
Indices: 8326--8350 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8316 TCTTCGGGGA
8326 CTTTTTCTTCTT
1 CTTTTTCTTCTT
8338 CTTTTTCTTCTT
1 CTTTTTCTTCTT
8350 C
1 C
8351 AGGATTATAT
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:8559 original size:24 final size:24
Alignment explanation
Indices: 8525--8571 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
8515 CTGAAACATC
8525 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
8549 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
8572 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:9281 original size:20 final size:20
Alignment explanation
Indices: 9253--9621 Score: 433
Period size: 20 Copynumber: 18.4 Consensus size: 20
9243 AAATTTAAGT
* * * *
9253 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
9273 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
9293 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
**
9313 GTTGCGATTTACGGATTA-TT
1 GTTGCGATTTACGGA-TACGC
9333 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9353 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
9373 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
9393 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9413 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9433 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
9453 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
9473 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9493 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
9513 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
* *
9533 GTTGTGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
9553 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
9573 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
9593 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
9613 GTTGCGATT
1 GTTGCGATT
9622 ATGGAAAATC
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 6 0.02
20 293 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:22133 original size:18 final size:19
Alignment explanation
Indices: 22110--22153 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
22100 CCAGTAATCC
*
22110 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
22128 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
22148 TATTCC
1 TATTCC
22154 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:22141 original size:20 final size:20
Alignment explanation
Indices: 22116--22153 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22106 ATCCTATTCC
*
22116 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
22136 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
22154 GTGAACCAAA
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:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:25128 original size:24 final size:24
Alignment explanation
Indices: 25096--25151 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
25086 CTATTTTTTC
25096 GCTTCAATTGAGCTCAAATCTTAG
1 GCTTCAATTGAGCTCAAATCTTAG
*
25120 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATCTTAG
25144 GCTTCAAT
1 GCTTCAAT
25152 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATCTTAG
Found at i:25411 original size:30 final size:30
Alignment explanation
Indices: 25375--25440 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
25365 AGTGAACCGG
*
25375 CGGTTCAAACCGGTTTTGCCGGTTTTCAGC
1 CGGTTCAAACCGATTTTGCCGGTTTTCAGC
** *
25405 CGGTTCACCCCGATTTTTCCGGTTTTCAGC
1 CGGTTCAAACCGATTTTGCCGGTTTTCAGC
25435 CGGTTC
1 CGGTTC
25441 TTCCGGTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.30, G:0.24, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTGCCGGTTTTCAGC
Found at i:30566 original size:22 final size:22
Alignment explanation
Indices: 30541--30582 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
30531 TTTCGTCCCA
*
30541 TATATATATATATTTTTTTAAT
1 TATATATATATATTTATTTAAT
* *
30563 TATATTTATTTATTTATTTA
1 TATATATATATATTTATTTA
30583 CTATATTCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TATATATATATATTTATTTAAT
Found at i:30597 original size:40 final size:40
Alignment explanation
Indices: 30553--30628 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
30543 TATATATATA
30553 TTTTTTTAATTATATT-TATTTATTTAT-TTACTATATTCCT
1 TTTTTTTAATTATATTATA-TTATTTATATTA-TATATTCCT
*
30593 TTTTTTTATTTATATTATATTATTTATATTATATAT
1 TTTTTTTAATTATATTATATTATTTATATTATATAT
30629 ATCTTATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
40 28 0.85
41 5 0.15
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (40 bp):
TTTTTTTAATTATATTATATTATTTATATTATATATTCCT
Found at i:30629 original size:2 final size:2
Alignment explanation
Indices: 30603--30674 Score: 82
Period size: 2 Copynumber: 38.0 Consensus size: 2
30593 TTTTTTTATT
* *
30603 TA TA T- TA TA T- TA TT TA TA T- TA TA TA TA TC T- TA TA TCA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
30641 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
30675 GATGTATTAA
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
1 5 0.08
2 54 0.89
3 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:30807 original size:42 final size:42
Alignment explanation
Indices: 30756--30886 Score: 119
Period size: 42 Copynumber: 3.1 Consensus size: 42
30746 ATTTTCTTAA
*
30756 TATTCTATTTTTGTTTTTATTTATTTATATATATTATATATT
1 TATTTTATTTTTGTTTTTATTTATTTATATATATTATATATT
* * * *
30798 TATTTTATTTTT-TATTTTATTTCTTAATATCATA-GATATCTT
1 TATTTTATTTTTGT-TTTTATTTATTTATAT-ATATTATATATT
* *
30840 TATTTT-TTTTTG-TTTTACTTAGTATTATATAT-TTATTATTTT
1 TATTTTATTTTTGTTTTTATTTA-T-TTATATATATTA-TATATT
30882 TATTT
1 TATTT
30887 GTTTTAGTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
40 7 0.10
41 10 0.14
42 52 0.72
43 3 0.04
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (42 bp):
TATTTTATTTTTGTTTTTATTTATTTATATATATTATATATT
Found at i:30879 original size:36 final size:36
Alignment explanation
Indices: 30786--30892 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 36
30776 TTATTTATAT
30786 ATATTATATATTTATTTTATTTTTTATTT-TATTT-CTTA
1 ATATTATATATTTA--TTATTTTTT-TTTGT-TTTACTTA
* *
30824 ATATCATAGATATCT-TTATTTTTTTTTGTTTTACTTA
1 ATAT--TATATATTTATTATTTTTTTTTGTTTTACTTA
* *
30861 GTATTATATATTTATTATTTTTATTTGTTTTA
1 ATATTATATATTTATTATTTTTTTTTGTTTTA
30893 GTAAATACTA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
35 7 0.12
36 23 0.40
37 17 0.29
38 4 0.07
40 7 0.12
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (36 bp):
ATATTATATATTTATTATTTTTTTTTGTTTTACTTA
Found at i:30937 original size:11 final size:11
Alignment explanation
Indices: 30921--30945 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30911 GTACACATTA
30921 TTTTAATTTCT
1 TTTTAATTTCT
30932 TTTTAATTTCT
1 TTTTAATTTCT
30943 TTT
1 TTT
30946 ACATTTTTTT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTAATTTCT
Found at i:31021 original size:19 final size:17
Alignment explanation
Indices: 30999--31041 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
30989 TGTTTCTTTG
30999 TTTTTTAACATTTTATTCA
1 TTTTTTAA-ATTTTATT-A
*
31018 TTTTGTTTAATTTTATTA
1 TTTT-TTAAATTTTATTA
31036 TTTTTT
1 TTTTTT
31042 TATTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 5 0.23
19 12 0.55
20 3 0.14
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTTTAAATTTTATTA
Found at i:31044 original size:11 final size:11
Alignment explanation
Indices: 31028--31052 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31018 TTTTGTTTAA
31028 TTTTATTATTT
1 TTTTATTATTT
31039 TTTTATTATTT
1 TTTTATTATTT
31050 TTT
1 TTT
31053 AGGTGTTTTG
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTATTT
Found at i:31049 original size:19 final size:18
Alignment explanation
Indices: 31027--31078 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
31017 ATTTTGTTTA
31027 ATTTTATTATTTTTTTATT
1 ATTTT-TTATTTTTTTATT
* * *
31046 ATTTTTTAGGTGTTTTGTT
1 ATTTTTTA-TTTTTTTATT
31065 ATTTTTTATTTTTT
1 ATTTTTTATTTTTT
31079 CTTGTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (18 bp):
ATTTTTTATTTTTTTATT
Found at i:31092 original size:26 final size:28
Alignment explanation
Indices: 31033--31093 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 28
31023 TTTAATTTTA
*
31033 TTATTT-TTTTATTATTTTTTAGGTGTT
1 TTATTTATTTTATTATTTTTTACGTGTT
* *
31060 TT-GTTATTTT-TTATTTTTT-CTTGTT
1 TTATTTATTTTATTATTTTTTACGTGTT
31085 TTATTTATT
1 TTATTTATT
31094 ATTCTCACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
25 6 0.21
26 16 0.57
27 6 0.21
ACGTcount: A:0.13, C:0.02, G:0.08, T:0.77
Consensus pattern (28 bp):
TTATTTATTTTATTATTTTTTACGTGTT
Found at i:34368 original size:69 final size:69
Alignment explanation
Indices: 34249--34386 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
34239 GATTTAAACT
34249 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
34314 TCAA
66 TCAA
* * * * *
34318 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGCATCAC-TCTACTCGAAGATCATGGAGC
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTC-ACTCGAAGATCATAGAGC
34382 ATCAA
65 ATCAA
34387 GAGAGAAACA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 2 0.03
69 61 0.97
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
TCAA
Found at i:35395 original size:32 final size:33
Alignment explanation
Indices: 35321--35413 Score: 125
Period size: 32 Copynumber: 2.8 Consensus size: 33
35311 TGAGGGCATC
*
35321 TTTGAAGATTCAACATCAAATGTTGGGACATTTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCATTTT
* *
35355 TTTTAGATTTAACATCAAATGTTGGGGCA-TTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTTT
* *
35387 TTTGAGATTCAACATCGAATATTGGGG
1 TTTGAGATTCAACATCAAATGTTGGGG
35414 TATCTTTGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
32 26 0.50
33 23 0.44
34 3 0.06
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (33 bp):
TTTGAGATTCAACATCAAATGTTGGGGCATTTT
Found at i:36248 original size:106 final size:106
Alignment explanation
Indices: 36059--36282 Score: 277
Period size: 106 Copynumber: 2.1 Consensus size: 106
36049 CGTGCCACTT
* * *
36059 GAGACAACACAAGTTCAACTTCACAACAAAGAGACGACTGGTTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAGCTCAACTTCACAACAAAGAGACGACTGGCTGTCAACAAACAATTTCCCAATC
*
36124 TCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGGACTC
66 CCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGGACTC
* * * * * * * *
36165 GAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCTAGTC
1 GAGACAACACAAGCTCAACTTCACAACAAAGAGACGACTGGCTGTCAACAAACAATTTCCCAATC
* ** * *
36230 CCAGAGCCAATTTTAACTTCATGGCGGAGGATATTGGACTC
66 CCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGGACTC
* *
36271 GAAACAATACAA
1 GAGACAACACAA
36283 CTTACTTGGA
Statistics
Matches: 98, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (106 bp):
GAGACAACACAAGCTCAACTTCACAACAAAGAGACGACTGGCTGTCAACAAACAATTTCCCAATC
CCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGGACTC
Found at i:36599 original size:36 final size:37
Alignment explanation
Indices: 36552--36739 Score: 112
Period size: 37 Copynumber: 5.4 Consensus size: 37
36542 ATTGAAAACA
* * *
36552 TTTCCCTTGAAATG-AATTTTATCTCGATTAAGATAG
1 TTTCCCTTGAAACGAAATTTTATCTCCATTAAGACAG
* * *
36588 TTTCCCTTGAAACGAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACGAAATTTTATCTCCATTAAGACAG
* * *
36625 TTTCTCTTGAAAC-ATAA--ATAT-T-GA--AA-ACA-
1 TTTCCCTTGAAACGA-AATTTTATCTCCATTAAGACAG
* ** *
36654 TTTCCCTTGAAA-TAAATTTTATCTCGC-TTGGGATAG
1 TTTCCCTTGAAACGAAATTTTATCTC-CATTAAGACAG
* * * *
36690 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAAATTTTATCTCCATTAAGACAG
*
36727 TTTCTCTTGAAAC
1 TTTCCCTTGAAAC
36740 ATAAACATTG
Statistics
Matches: 115, Mismatches: 23, Indels: 27
0.70 0.14 0.16
Matches are distributed among these distances:
28 2 0.02
29 12 0.10
30 6 0.05
31 2 0.02
34 1 0.01
35 4 0.03
36 27 0.23
37 61 0.53
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACGAAATTTTATCTCCATTAAGACAG
Found at i:36606 original size:102 final size:102
Alignment explanation
Indices: 36500--36869 Score: 605
Period size: 102 Copynumber: 3.6 Consensus size: 102
36490 TTTTGGAACT
* *
36500 AAATTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* * *
36565 GAATTTTATCTCGATTAAGATAGTTTCCCTTGAAACG
66 GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
* *
36602 AAATTTTGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAACATTTCCCTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
* *
36667 AAATTTTATCTCGCTTGGGATAGTTTCCCTTGAAACA
66 GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
*
36704 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAAT
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
*
36769 GAATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACA
66 GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
* * * *
36806 AAATTTTGTTTCCCTTGAGATAGTTTCTCTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAA
36870 CACAAAATAT
Statistics
Matches: 248, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 248 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (102 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
Found at i:36729 original size:37 final size:37
Alignment explanation
Indices: 36654--36842 Score: 139
Period size: 37 Copynumber: 5.4 Consensus size: 37
36644 ATTGAAAACA
* * *
36654 TTTCCCTTGAAA-TAAATTTTATCTCGCTTGGGATAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGATAG
* *
36690 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGATAG
* * * * *
36727 TTTCTCTTGAAACATAA----A----CATTGA-AAACA
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGATA-G
* ** *
36756 TTTCCTTTGAAA-TGAATTTTATCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGATAG
* *
36792 TTTCCCTTGAAACAAAATTTTGTTTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGATAG
*
36829 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
36843 TAAACCTTGA
Statistics
Matches: 115, Mismatches: 26, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
28 4 0.03
29 15 0.13
32 1 0.01
36 27 0.23
37 68 0.59
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGATAG
Found at i:36982 original size:36 final size:37
Alignment explanation
Indices: 36907--37009 Score: 190
Period size: 36 Copynumber: 2.8 Consensus size: 37
36897 AAAACGAGTT
36907 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
*
36944 TTGAGACGGTTTCCCTTGAAACAAAAT-TTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
36980 TTGAGACAGTTTCCCTTGAAACAAAATCTT
1 TTGAGACAGTTTCCCTTGAAACAAAATCTT
37010 TGAATATCTT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 35 0.56
37 28 0.44
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATCTTGTCTCTC
Found at i:37026 original size:102 final size:102
Alignment explanation
Indices: 36920--37106 Score: 245
Period size: 102 Copynumber: 1.8 Consensus size: 102
36910 AGACAGTTTC
* **
36920 CCTTGAAACAAAATCTT-GTCTCTCTTGAGACGGTTTCCCTTGA-AAC-AAAATTTGTCTCTCTT
1 CCTTGAAAC-AAAT-TTCGTCTCCCTTGAGACAATTT-CCTTGAGAACTAAAATTTGTCTCTCTT
36982 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
63 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * **
37022 CCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTAGAACTAAGTTTTGTCTCTCTTGAG
1 CCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCTTGAGAACTAAAATTTGTCTCTCTTGAG
**
37087 ACAGTTTCTTTTGAAACAAA
66 ACAGTTTCCCTTGAAACAAA
37107 TTTTGTCCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 6 0.08
101 23 0.32
102 44 0.60
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (102 bp):
CCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCTTGAGAACTAAAATTTGTCTCTCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:37085 original size:37 final size:36
Alignment explanation
Indices: 37024--37140 Score: 155
Period size: 36 Copynumber: 3.2 Consensus size: 36
37014 TATCTTTTCC
* * *
37024 TTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
*
37060 TT-AGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
37097 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
37133 TTGAAACA
1 TTGAAACA
37141 CAAAAAAACC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 1 0.01
36 39 0.55
37 30 0.42
38 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:37202 original size:39 final size:36
Alignment explanation
Indices: 37126--37218 Score: 120
Period size: 39 Copynumber: 2.6 Consensus size: 36
37116 TCTTGAGACA
*
37126 GTTTCTCTTG-AA-ACACAAAAAAACCCTCGAAATT
1 GTTTCTCTTGAAACACACAAAAAAACCCTCGAAAAT
*
37160 GTTTCTCTTGAAACACACACACAAAAACCCTTTGAAAAT
1 GTTTCTCTTGAAACACACA-A-AAAAACCC-TCGAAAAT
37199 GTTTCTCTTGAAACAC-CAAA
1 GTTTCTCTTGAAACACACAAA
37219 CCTTCGAGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
34 10 0.19
35 2 0.04
36 6 0.12
37 2 0.04
38 10 0.19
39 22 0.42
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.27
Consensus pattern (36 bp):
GTTTCTCTTGAAACACACAAAAAAACCCTCGAAAAT
Found at i:38389 original size:14 final size:14
Alignment explanation
Indices: 38366--38433 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
38356 TATTCCTCTT
38366 TTAT-TTATTTATA
1 TTATATTATTTATA
*
38379 TTATATTATTTTTA
1 TTATATTATTTATA
38393 TTATATATATCTTATA
1 TTATAT-TAT-TTATA
* *
38409 TCATTATATATATATA
1 TTA-TAT-TATTTATA
38425 TATATATTA
1 T-TATATTA
38434 ATTTTTCTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
13 4 0.09
14 14 0.31
15 5 0.11
16 14 0.31
17 8 0.18
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATATTATTTATA
Found at i:38433 original size:19 final size:18
Alignment explanation
Indices: 38371--38433 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
38361 CTCTTTTATT
38371 TATT-TATATTATAT-TA
1 TATTATATATTATATATA
38387 T-TT-T-TATTATATATA
1 TATTATATATTATATATA
*
38402 TCTTATATCATTATATATA
1 TATTATAT-ATTATATATA
38421 TATATATATATTA
1 TAT-TATATATTA
38434 ATTTTTCTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
14 8 0.20
15 6 0.15
16 3 0.08
17 1 0.03
18 1 0.03
19 16 0.40
20 5 0.12
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATATATTATATATA
Found at i:38508 original size:11 final size:12
Alignment explanation
Indices: 38487--38576 Score: 53
Period size: 12 Copynumber: 7.4 Consensus size: 12
38477 ATTTTATACG
38487 TTTTTATATATT
1 TTTTTATATATT
38499 TTTTTA-ATATT
1 TTTTTATATATT
* *
38510 CTAATTTTGCTTTATT
1 -T--TTTT-ATATATT
*
38526 TATTTATATA--
1 TTTTTATATATT
* *
38536 TATATATATATT
1 TTTTTATATATT
*
38548 TTTTTATTTATT
1 TTTTTATATATT
38560 TTTTCTAT-TATT
1 TTTT-TATATATT
38572 TTTTT
1 TTTTT
38577 TCTTAATATC
Statistics
Matches: 61, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
10 9 0.15
11 6 0.10
12 31 0.51
13 6 0.10
14 4 0.07
15 1 0.02
16 4 0.07
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.71
Consensus pattern (12 bp):
TTTTTATATATT
Found at i:38803 original size:11 final size:11
Alignment explanation
Indices: 38787--38812 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38777 ATTTTGTTTA
38787 TTTTTATTATT
1 TTTTTATTATT
38798 TTTTTATTATT
1 TTTTTATTATT
38809 TTTT
1 TTTT
38813 ACGTGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:38810 original size:19 final size:18
Alignment explanation
Indices: 38679--38838 Score: 65
Period size: 19 Copynumber: 8.2 Consensus size: 18
38669 GTACACATTA
38679 TTTTTATTATTTTTTAATT
1 TTTTTATTATTTTTT-ATT
*
38698 TCTTTTACCTTTTTTTTTTATT
1 T-TTTTA---TTATTTTTTATT
* *
38720 TTTTTACTCTATTAAATTT-TC
1 TTTTTA-T-TATT--TTTTATT
* *
38741 TCTTTATTTATGTCTTTA-T
1 TTTTTA-TTAT-TTTTTATT
**
38760 TTTTTAACATTTTATTCATT
1 TTTTTATTATTTT-TT-ATT
*
38780 TTGTTTATT-TTTATTATT
1 TT-TTTATTATTTTTTATT
*
38798 TTTTTATTATTTTTTACGT
1 TTTTTATTATTTTTTA-TT
* *
38817 GTTTTATTATTTTTCATT
1 TTTTTATTATTTTTTATT
38835 TTTT
1 TTTT
38839 CTTGTTTTAT
Statistics
Matches: 104, Mismatches: 22, Indels: 31
0.66 0.14 0.20
Matches are distributed among these distances:
17 8 0.08
18 19 0.18
19 28 0.27
20 17 0.16
21 17 0.16
22 7 0.07
23 8 0.08
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTATTATTTTTTATT
Found at i:38852 original size:26 final size:28
Alignment explanation
Indices: 38793--38853 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
38783 TTTATTTTTA
*
38793 TTATTT-TTTTATTATTTTTTACGTGTT
1 TTATTTATTTTATCATTTTTTACGTGTT
*
38820 TTA-TTATTTT-TCATTTTTT-CTTGTT
1 TTATTTATTTTATCATTTTTTACGTGTT
38845 TTATTTATT
1 TTATTTATT
38854 ATTCTCACGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 8 0.27
26 15 0.50
27 7 0.23
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (28 bp):
TTATTTATTTTATCATTTTTTACGTGTT
Found at i:42970 original size:70 final size:70
Alignment explanation
Indices: 42882--43015 Score: 241
Period size: 70 Copynumber: 1.9 Consensus size: 70
42872 TGTTCTGTGT
*
42882 GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATTCTACCATTTGAATTTTACAT
1 GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACAT
42947 GATCC
66 GATCC
* *
42952 GCTTATTTCTATATGTATATTTGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACA
1 GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACA
43016 CTGTTTTTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (70 bp):
GCTTATTGCTATATGTATATTAGATTACATCTGTTATGGTTAATGCTACCATTTGAATTTTACAT
GATCC
Found at i:46109 original size:23 final size:23
Alignment explanation
Indices: 46079--46125 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
46069 GCAATTAAGG
46079 CAAGCAAACAAAACATCGTCGTA
1 CAAGCAAACAAAACATCGTCGTA
46102 CAAGCAAACAAAACATCGTCGTA
1 CAAGCAAACAAAACATCGTCGTA
46125 C
1 C
46126 TTTGGTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.28, G:0.13, T:0.13
Consensus pattern (23 bp):
CAAGCAAACAAAACATCGTCGTA
Found at i:49669 original size:21 final size:22
Alignment explanation
Indices: 49632--49672 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
49622 ACACGTTTTA
*
49632 CTCTACTATTGTGGCATGTTTC
1 CTCTACTATTATGGCATGTTTC
49654 CTCTACT-TTATGGCATGTT
1 CTCTACTATTATGGCATGTT
49673 GTTCGCTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (22 bp):
CTCTACTATTATGGCATGTTTC
Done.