Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005208.1 Hibiscus syriacus cultivar Beakdansim tig00011776_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: 91090
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4723 original size:11 final size:11
Alignment explanation
Indices: 4707--4731 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4697 ATTTGAAATC
4707 AAAAAAGAAAA
1 AAAAAAGAAAA
4718 AAAAAAGAAAA
1 AAAAAAGAAAA
4729 AAA
1 AAA
4732 GGGAAAGGCT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:6124 original size:42 final size:42
Alignment explanation
Indices: 6047--6150 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
6037 AGGTCTTATG
* * * *
6047 GATGGCCCGAAGTAC-TAATCATCTTGCTCGAAAGACTTA-T
1 GATGACCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACT
* *
6087 AGGTGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 -GATGACCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACT
*
6130 GATGGCCCGAAGGACTTAAGC
1 GATGACCCGAAGGACTTAAGC
6151 TGATTCGAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 11 0.21
42 40 0.77
43 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (42 bp):
GATGACCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACT
Found at i:6260 original size:59 final size:59
Alignment explanation
Indices: 6153--6303 Score: 221
Period size: 59 Copynumber: 2.5 Consensus size: 59
6143 ACTTAAGCTG
* *
6153 ATTCGAAGTGTTGTGAATCGAGCAATAGAAAATGTTAACCCCTCTGGTGAGGCGTTGCTA
1 ATTCGAAGTGTTGTGAATCGAGCAA-AGAAAATGTTAACCCCTATGGTGAGGCGTTACTA
* * * *
6213 ATTTGAAGTGTTGTGAATTGAGCAAATAAAATGTTAACCCCTATGGTGAGGCGTTACTG
1 ATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTAACCCCTATGGTGAGGCGTTACTA
* *
6272 ATTCGAAGTGTAGTGAATCGAGCAAAGGAAAT
1 ATTCGAAGTGTTGTGAATCGAGCAAAGAAAAT
6304 ATTGAAAATG
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 57 0.71
60 23 0.29
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (59 bp):
ATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTAACCCCTATGGTGAGGCGTTACTA
Found at i:6404 original size:42 final size:42
Alignment explanation
Indices: 6353--6437 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
6343 AATGACTTAT
* *
6353 CATCTTGCTC-AAAAGACTTA-TAGATGACTCGAAGGATTTAAG
1 CATCATGCTCGAAAA-ACTTACT-GATGACTCGAAGGACTTAAG
*
6395 CATCATGCTCGAAAAACTTACTGATGGCTCGAAGGACTTAAG
1 CATCATGCTCGAAAAACTTACTGATGACTCGAAGGACTTAAG
6437 C
1 C
6438 TGATTCGAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 33 0.87
43 5 0.13
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (42 bp):
CATCATGCTCGAAAAACTTACTGATGACTCGAAGGACTTAAG
Found at i:6416 original size:287 final size:285
Alignment explanation
Indices: 5926--6720 Score: 1149
Period size: 287 Copynumber: 2.8 Consensus size: 285
5916 TTCGTTGTTG
* * * * *
5926 ATTCGTAGTGTTGTGAATCGAGCGAAGGAAATGTTAACCCCTCTGGTGGGGCATTACGGATTTGA
1 ATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTAACCCCTCTGGTGGGGCATTACTGATTCGA
* * * *
5991 ATTGTTGTGAATTGAACAAAGAAAATGTTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCG
66 AGTGTTGTGAATCGAGCAAAGAAAATGTTGAAAATATCCT-CCCGAAGGTCTTATGGATGGCCCG
* * *
6056 AAGTACTAATCATCTTGCTCGAAAGACTTATAGGTGACCCGAAGGATTTAAGCATCATGCTCGAA
130 AAG-ACTTATCATCTTGCTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAA
6121 AGACTTACTGATGGCCCGAAGGACTTAAGCTGATTCGAAGTGTTGTGAATCGAGCAATAGAAAAT
194 AGACTTACTGATGGCCCGAAGGACTTAAGCTGATTCGAAGTGTTGTGAATCGAGCAATAGAAAAT
*
6186 GTTAACCCCTCTGGTGAGGCGTTGCTA
259 GTTAACCCCTCTGGTGAGGCATTGCTA
* * * * * *
6213 ATTTGAAGTGTTGTGAATTGAGCAAATAAAATGTTAACCCCTATGGTGAGGCGTTACTGATTCGA
1 ATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTAACCCCTCTGGTGGGGCATTACTGATTCGA
* * * * * *
6278 AGTGTAGTGAATCGAGCAAAGGAAATATTGAAAATGTCTTGCCCAAAGGTCTTATGGATGGCCCG
66 AGTGTTGTGAATCGAGCAAAGAAAATGTTGAAAATATCCT-CCCGAAGGTCTTATGGATGGCCCG
*
6343 AATGACTTATCATCTTGCTCAAAAGACTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAA
130 AA-GACTTATCATCTTGCTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAA
* * *
6408 AAACTTACTGATGGCTCGAAGGACTTAAGCTGATTCGAAGTGTTGTGAATCGAGCAATAGGAAAT
194 AGACTTACTGATGGCCCGAAGGACTTAAGCTGATTCGAAGTGTTGTGAATCGAGCAATAGAAAAT
* *
6473 GTTAACCCCTCTGGTGGGGTATTGCTA
259 GTTAACCCCTCTGGTGAGGCATTGCTA
* * * * * **
6500 ATTCGAAGTGTTATGAATCGAGCAAAGAAAATGTTAAACACTCTAGTGGGGTATTGTTGATTCGA
1 ATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTAACCCCTCTGGTGGGGCATTACTGATTCGA
* * *
6565 AGTGTTGTGAATCGAGCAAAGAAAATGTTGAAAATATCCTCACGATGGTCTTATGGATGGTCCGA
66 AGTGTTGTGAATCGAGCAAAGAAAATGTTGAAAATATCCTCCCGAAGGTCTTATGGATGGCCCGA
* *
6630 AGGACTTATCATCTTGCTCGAAAGACTTATAGATGAATTGAAGGATTTAAGCATCATGCTCGAAA
131 A-GACTTATCATCTTGCTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAA
*
6695 GACTTACTGATGGCCCGAATGACTTA
195 GACTTACTGATGGCCCGAAGGACTTA
6721 CTCACCAAGA
Statistics
Matches: 446, Mismatches: 61, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
286 105 0.24
287 340 0.76
288 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (285 bp):
ATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTAACCCCTCTGGTGGGGCATTACTGATTCGA
AGTGTTGTGAATCGAGCAAAGAAAATGTTGAAAATATCCTCCCGAAGGTCTTATGGATGGCCCGA
AGACTTATCATCTTGCTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAG
ACTTACTGATGGCCCGAAGGACTTAAGCTGATTCGAAGTGTTGTGAATCGAGCAATAGAAAATGT
TAACCCCTCTGGTGAGGCATTGCTA
Found at i:6563 original size:59 final size:59
Alignment explanation
Indices: 6436--6593 Score: 244
Period size: 59 Copynumber: 2.7 Consensus size: 59
6426 AAGGACTTAA
* * * *
6436 GCTGATTCGAAGTGTTGTGAATCGAGCAATAGGAAATGTTAACCCCTCTGGTGGGGTATT
1 GCTGATTCGAAGTGTTGTGAATCGAGCAA-AGAAAATGTTAAACACTCTAGTGGGGTATT
* *
6496 GCTAATTCGAAGTGTTATGAATCGAGCAAAGAAAATGTTAAACACTCTAGTGGGGTATT
1 GCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTAAACACTCTAGTGGGGTATT
*
6555 GTTGATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTT
1 GCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTT
6594 GAAAATATCC
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 62 0.70
60 27 0.30
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (59 bp):
GCTGATTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTAAACACTCTAGTGGGGTATT
Found at i:6858 original size:57 final size:55
Alignment explanation
Indices: 6779--7027 Score: 176
Period size: 52 Copynumber: 4.6 Consensus size: 55
6769 ATTTTTAGAT
*
6779 ATCATCAAGAAGCCCCTAAAAATTAGGCTTAACTTCTTTAAAAATTCTTCAAAAATA
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTAAAAATTCTT--AAAATA
* * * ** * * **
6836 ATCATCAAGAAACCCATGAAAATCAGGCTT-TGTT-TCTAAAAACTCATTTGAA-A
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTAAAAATTC-TTAAAATA
* * * * *
6889 A-CATCAAGAAACCCCTTAAAATTAGGCTTAGCTTCTGTTAAAAATTAATTGGAAATC
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCT-TTAAAAATT-CTT-AAAATA
* * * **
6946 ATCATCAAGAATCCCCTAAAAATTAGGCTT-AGTT-TCT-AAAATCTCATTTGAA-A
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTAAAAAT-TC-TTAAAATA
6999 A-CATCAAGAAACCCCT-AAAATTAGGCTTA
1 ATCATCAAGAAACCCCTAAAAATTAGGCTTA
7028 GTTTATTTTA
Statistics
Matches: 150, Mismatches: 31, Indels: 27
0.72 0.15 0.13
Matches are distributed among these distances:
51 12 0.08
52 39 0.26
53 5 0.03
54 10 0.07
55 22 0.15
56 7 0.05
57 29 0.19
58 26 0.17
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (55 bp):
ATCATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTAAAAATTCTTAAAATA
Found at i:6910 original size:52 final size:52
Alignment explanation
Indices: 6838--7054 Score: 229
Period size: 52 Copynumber: 4.0 Consensus size: 52
6828 CAAAAATAAT
* * * *
6838 CATCAAGAAACCCATGAAAATCAGGCTTTGTTTCTAAAAACTCATTTGAAAA
1 CATCAAGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAAACTCATTTGAAAA
* * * *
6890 CATCAAGAAACCCCTTAAAATTAGGCTTAGCTTCTGTTAAAAATTAATTGGAAATCA
1 CATCAAGAAACCCCTTAAAATTAGGCTTAG-TT-T-CTAAAAACTCATTTGAAA--A
* * *
6947 TCATCAAGAATCCCCTAAAAATTAGGCTTAGTTTCTAAAATCTCATTTGAAAA
1 -CATCAAGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAAACTCATTTGAAAA
* *
7000 CATCAAGAAACCCC-TAAAATTAGGCTTAGTTTATTTTAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTTAAAATTAGGCTTAG--T-TTCTAAAAACTCATTTGAAAA
7054 C
1 C
7055 CTCCTATCAA
Statistics
Matches: 136, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
51 14 0.10
52 39 0.29
53 4 0.03
54 20 0.15
55 27 0.20
56 1 0.01
57 3 0.02
58 28 0.21
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (52 bp):
CATCAAGAAACCCCTTAAAATTAGGCTTAGTTTCTAAAAACTCATTTGAAAA
Found at i:6924 original size:109 final size:108
Alignment explanation
Indices: 6726--7044 Score: 370
Period size: 110 Copynumber: 2.9 Consensus size: 108
6716 ACTTACTCAC
* * * * *
6726 CAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAAAATCTTTCATTTTTAGATATCATCAAGAAG
1 CAAGAAACCCATGAAAATCAGGCTTAGTTTC-TAAAATC--TCA--TTT-GAAAACATCAAGAAA
* *
6791 CCCCTAAAAATTAGGCTTAACTTCTTTAAAAATTCTTCAAAAATAATCAT
60 CCCCTTAAAATTAGGCTTAGCTTCTTTAAAAATTCTT-AAAAATAATCAT
* *
6841 CAAGAAACCCATGAAAATCAGGCTTTGTTTCTAAAAACTCATTTGAAAACATCAAGAAACCCCTT
1 CAAGAAACCCATGAAAATCAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCAAGAAACCCCTT
* ** *
6906 AAAATTAGGCTTAGCTTCTGTTAAAAATTAATTGGAAATCATCAT
66 AAAATTAGGCTTAGCTTCT-TTAAAAATT-CTTAAAAATAATCAT
* * * *
6951 CAAGAATCCCCTAAAAATTAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCAAGAAACCCC-T
1 CAAGAAACCCATGAAAATCAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCAAGAAACCCCTT
* *
7015 AAAATTAGGCTTAGTTTATTTTAAAAATTC
66 AAAATTAGGCTTAGCTT-CTTTAAAAATTC
7045 ATTTGAAAAC
Statistics
Matches: 179, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
109 61 0.34
110 79 0.44
111 2 0.01
112 3 0.02
114 6 0.03
115 28 0.16
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (108 bp):
CAAGAAACCCATGAAAATCAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCAAGAAACCCCTT
AAAATTAGGCTTAGCTTCTTTAAAAATTCTTAAAAATAATCAT
Found at i:13463 original size:21 final size:22
Alignment explanation
Indices: 13437--13485 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
13427 AGAGCGTGGG
13437 GGGAATCA-ATACCCCCTCATA
1 GGGAATCAGATACCCCCTCATA
*
13458 GGGAAT-AGATACCCGCTCATA
1 GGGAATCAGATACCCCCTCATA
13479 GGGAATC
1 GGGAATC
13486 GGTTCCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (22 bp):
GGGAATCAGATACCCCCTCATA
Found at i:13607 original size:21 final size:21
Alignment explanation
Indices: 13582--13624 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13572 CAAACCATTA
13582 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
* *
13603 GGGGGAATCGGTTCCCTCTGG
1 GGGGGAATCGGTACCCCCTGG
13624 G
1 G
13625 CAATCTGCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.26, G:0.44, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:17469 original size:3 final size:3
Alignment explanation
Indices: 17461--17505 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
17451 TTGGTTTGTA
* *
17461 AAT AAT AAT AAT ATT TAT AAT -AT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17506 TATGGTAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:23867 original size:11 final size:11
Alignment explanation
Indices: 23851--23880 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
23841 TTGAGACATT
*
23851 ATCCGCCCCGC
1 ATCCGCCCCAC
23862 ATCCGCCCCAC
1 ATCCGCCCCAC
23873 ATCCGCCC
1 ATCCGCCC
23881 GCCCAGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.63, G:0.13, T:0.10
Consensus pattern (11 bp):
ATCCGCCCCAC
Found at i:32351 original size:31 final size:31
Alignment explanation
Indices: 32281--32356 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
32271 TCAAAAAACA
* *
32281 TAAGATATGATCACTTTCGTTTTTAATTAGT
1 TAAGATATGATCACTTTCATTTTTAATTAAT
*
32312 TAAGATATGTTCACTTTCATTTTT-ATTCAAT
1 TAAGATATGATCACTTTCATTTTTAATT-AAT
* *
32343 TAATATATGGTCAC
1 TAAGATATGATCAC
32357 CCTGAGTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 3 0.08
31 36 0.92
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (31 bp):
TAAGATATGATCACTTTCATTTTTAATTAAT
Found at i:32647 original size:24 final size:23
Alignment explanation
Indices: 32598--32668 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 23
32588 TTATATATAT
*
32598 ATATATATATATATTAACTTAAAA
1 ATATAT-TTTATATTAACTTAAAA
* * *
32622 ATATTTTTTATATTTACTTATTAA
1 ATATATTTTATATTAACTTA-AAA
32646 ATATATTTTATTATTAACTTAAA
1 ATATATTTTA-TATTAACTTAAA
32669 TTTAAAATAG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 12 0.32
24 17 0.45
25 9 0.24
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATTTTATATTAACTTAAAA
Found at i:32650 original size:17 final size:17
Alignment explanation
Indices: 32630--32662 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
32620 AAATATTTTT
32630 TATA-TTTACTTATTAAA
1 TATATTTTA-TTATTAAA
32647 TATATTTTATTATTAA
1 TATATTTTATTATTAA
32663 CTTAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATTATTAAA
Found at i:34092 original size:18 final size:17
Alignment explanation
Indices: 34051--34095 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
34041 ATATCTATCG
34051 AAATGATTTTTCTTAAA
1 AAATGATTTTTCTTAAA
34068 AAA-GATTAATTT-TTAAA
1 AAATGATT--TTTCTTAAA
34085 AAATGATTTTT
1 AAATGATTTTT
34096 AAAAGATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.28
17 11 0.44
18 7 0.28
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
AAATGATTTTTCTTAAA
Found at i:37321 original size:133 final size:133
Alignment explanation
Indices: 37042--37538 Score: 667
Period size: 133 Copynumber: 3.7 Consensus size: 133
37032 ATGAAATTTG
* * * * * * * *
37042 AAAAGGGGTCTGCTCCGTTGC-TCTTTAGAGTAGATTAGATATGAAAATGTTGATTCATTCCACT
1 AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCACT
* * * *
37106 ACTT-TTCAGGGAAGATTGAATCAAGGCAGACTTGTTCCATTGCTTCTCAGGGAAGATCAAATAT
66 -GTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGCTCCTCAGGGAAGATCAAATAT
37170 GG-A
130 GGAA
* *
37173 AAAAGAGGATATGCTCCACTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCAC
1 AAAAG-GGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCAC
* * * * *
37238 TGTTCTTCAGGGAAGATTGATTCGAGGTAGACTTGTTCAACTACTCCTCAAGGAAGATCAAATAT
65 TGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGCTCCTCAGGGAAGATCAAATAT
37303 GGAA
130 GGAA
* *
37307 AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCATATATGGAAACGTTGATTCATTCAACT
1 AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCACT
* * * * * *
37372 ATTCTTCAGGGAAAATTGAATCTAGGCAGACTTGTTCCACTGCTCCTTAGGGAAGATCAATTTTG
66 GTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGCTCCTCAGGGAAGATCAAATATG
37437 GAA
131 GAA
* * * *
37440 AAAAAGGATCTGCTCCGCTGCTTCTTCAGGGTAAATTAGATCTGGAAATGTTGATTCATTCCACT
1 AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCACT
*
37505 GTTCTTCAGGGAAGATTGAATCGAGACAGACTTG
66 GTTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
37539 CTTATCTTGT
Statistics
Matches: 318, Mismatches: 44, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
131 5 0.02
132 14 0.04
133 293 0.92
134 6 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (133 bp):
AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCACT
GTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGCTCCTCAGGGAAGATCAAATATG
GAA
Found at i:38895 original size:35 final size:38
Alignment explanation
Indices: 38822--38895 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 38
38812 GGGTCTTTTT
* *
38822 CTCCCCATTTTTTGATTCGATAGAAGCATTGTAGAGGGG
1 CTCCCCATTTTTTGATTCGA-AGAAGCAATGTAAAGGGG
38861 CTCCCCATTTTTT-ATTCG-A-AAGCAATGTAAAGGGG
1 CTCCCCATTTTTTGATTCGAAGAAGCAATGTAAAGGGG
38896 TTTTCTTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 14 0.42
36 1 0.03
38 5 0.15
39 13 0.39
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (38 bp):
CTCCCCATTTTTTGATTCGAAGAAGCAATGTAAAGGGG
Found at i:48459 original size:174 final size:176
Alignment explanation
Indices: 48149--48476 Score: 500
Period size: 174 Copynumber: 1.9 Consensus size: 176
48139 GAGCAAGATG
* * * * *
48149 ATAAGACCTTCGGACATGTTGTTTTCACGTGATTTTCAAAAAATGAGAAAGCGGTTTCCAAAGTT
1 ATAAGACCTTCGGACAGGATGTTTTCACGTGATTTTCAAAAAATAAGAAAGCGATTTCCAAAGTG
* *
48214 TCTTATTTAAGTATTTTTAGAAAATGAAATATTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCT
66 TCTCATTTAAGTATTTTCAGAAAATGAAATATTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCT
48279 TACCCAGTAAACTATTTCCAAAATTGGCAAGTTCTTCGAGCCATCT
131 TACCCAGTAAACTATTTCCAAAATTGGCAAGTTCTTCGAGCCATCT
* ** * *
48325 ATAAGACCTTCGG-CAGGATGTTTTCATGTGATTTTTTAAAAATAAGAAAGCGATTTTCAATGTG
1 ATAAGACCTTCGGACAGGATGTTTTCACGTGATTTTCAAAAAATAAGAAAGCGATTTCCAAAGTG
* *
48389 TCTCATTT-AGTATTTTCAGAAAATGACATTTTTGAAAAGTAAGAAA-ACGATTTCCAAAGTTTC
66 TCTCATTTAAGTATTTTCAGAAAATGAAATATTTGAAAAGTAAGAAAGA-GATTTCCAAAGTTTC
48452 TTACCCAGTAAACTATTTCCAAAAT
130 TTACCCAGTAAACTATTTCCAAAAT
48477 CCATAAGTCA
Statistics
Matches: 137, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
173 1 0.01
174 75 0.55
175 48 0.35
176 13 0.09
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (176 bp):
ATAAGACCTTCGGACAGGATGTTTTCACGTGATTTTCAAAAAATAAGAAAGCGATTTCCAAAGTG
TCTCATTTAAGTATTTTCAGAAAATGAAATATTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCT
TACCCAGTAAACTATTTCCAAAATTGGCAAGTTCTTCGAGCCATCT
Found at i:49652 original size:41 final size:41
Alignment explanation
Indices: 49548--49652 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 41
49538 TTTCCAAAAT
* * * * * *
49548 TGATAAGTCCTTTGGGCCATCAATAAATCTTTTGAGCATGA
1 TGATAAATCCTTCGGGCCATCTATAAAGCTTTCGAGCAAGA
* * * *
49589 TGATTACATCCTTCGGGTCATCTATCAGGCTTTCGAGCAAGA
1 TGA-TAAATCCTTCGGGCCATCTATAAAGCTTTCGAGCAAGA
49631 TGATAAATCCTTCGGGCCATCT
1 TGATAAATCCTTCGGGCCATCT
49653 GTAAGACCTT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
41 20 0.39
42 31 0.61
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (41 bp):
TGATAAATCCTTCGGGCCATCTATAAAGCTTTCGAGCAAGA
Found at i:50974 original size:36 final size:38
Alignment explanation
Indices: 50900--50974 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
50890 GGGTCTTCTT
* *
50900 CTCCCCATTTTTTGATTTGATAGAAGCATTGTAGAGGGG
1 CTCCCCATTTTTTGATTTGA-AGAAGCAATGTAAAGGGG
50939 CTCCCCATTTTTTGATTTG-A-AAGCAATGTAAAGGGG
1 CTCCCCATTTTTTGATTTGAAGAAGCAATGTAAAGGGG
50975 TTTTCTTCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 14 0.41
37 1 0.03
39 19 0.56
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (38 bp):
CTCCCCATTTTTTGATTTGAAGAAGCAATGTAAAGGGG
Found at i:51599 original size:10 final size:10
Alignment explanation
Indices: 51584--51658 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
51574 CATTTAATAA
51584 ATAAACGAAC
1 ATAAACGAAC
51594 ATAAACG---
1 ATAAACGAAC
51601 A-AAACGAAC
1 ATAAACGAAC
51610 ATAAACGAAC
1 ATAAACGAAC
** *
51620 ACGAAC-ATAA
1 ATAAACGA-AC
51630 ATGAACACGAAC
1 AT-AA-ACGAAC
51642 ATAAACGAAC
1 ATAAACGAAC
51652 ATAAACG
1 ATAAACG
51659 TTGGAGGCCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 5 0.10
7 1 0.02
9 2 0.04
10 34 0.67
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:51651 original size:16 final size:16
Alignment explanation
Indices: 51588--51652 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
51578 TAATAAATAA
*
51588 ACGAACATAAACGAAA
1 ACGAACATAAACGAAC
51604 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
51620 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
51636 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
51652 A
1 A
51653 TAAACGTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:52419 original size:14 final size:14
Alignment explanation
Indices: 52402--52457 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
52392 AATGAACATA
*
52402 AACGAACATAATCG
1 AACGAACATAACCG
52416 AACGAACAT----G
1 AACGAACATAACCG
*
52426 AACGAACATAACCA
1 AACGAACATAACCG
52440 AACGAACATAACCG
1 AACGAACATAACCG
52454 AACG
1 AACG
52458 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 10 0.28
14 26 0.72
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:52422 original size:24 final size:24
Alignment explanation
Indices: 52382--52456 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
52372 GATTGTGTTA
*
52382 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
52406 AACATAATCGAACGAACATGAACG
1 AACATAATCGAACGAACATAAACG
* * *
52430 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
52454 AAC
1 AAC
52457 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:53404 original size:44 final size:44
Alignment explanation
Indices: 53318--53415 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
53308 TTTGTGCTTA
*
53318 ATGCATCGATACACTGAACAGTGCATCGATACATCCCTTTGAAT
1 ATGCATCGATACACTGAACAGTGCACCGATACATCCCTTTGAAT
* *
53362 ATGCATCGATACACCATGAA-GGTGCACCGATGCA-CTCC-TTGAAT
1 ATGCATCGATACA-C-TGAACAGTGCACCGATACATC-CCTTTGAAT
*
53406 GTGCATCGAT
1 ATGCATCGAT
53416 GCATCCGTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 29 0.62
45 14 0.30
46 4 0.09
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (44 bp):
ATGCATCGATACACTGAACAGTGCACCGATACATCCCTTTGAAT
Found at i:54597 original size:22 final size:22
Alignment explanation
Indices: 54572--54626 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
54562 CATTACCATT
54572 TAATTAAAAATTAATCAAGAGA
1 TAATTAAAAATTAATCAAGAGA
54594 TAATTAAAAATTAATCAAGAGA
1 TAATTAAAAATTAATCAAGAGA
54616 TAATTAAAAAT
1 TAATTAAAAAT
54627 GTGCTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (22 bp):
TAATTAAAAATTAATCAAGAGA
Found at i:55474 original size:7 final size:7
Alignment explanation
Indices: 55462--55511 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
55452 TTTTTCTTTA
55462 TTTTTCT
1 TTTTTCT
55469 TTTTTCT
1 TTTTTCT
*
55476 TTTTCCT
1 TTTTTCT
*
55483 TTTTCCT
1 TTTTTCT
55490 TTTTTC-
1 TTTTTCT
* *
55496 ATTTTCC
1 TTTTTCT
55503 TTTTTCT
1 TTTTTCT
55510 TT
1 TT
55512 CTTCAGGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:55484 original size:14 final size:14
Alignment explanation
Indices: 55462--55511 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
55452 TTTTTCTTTA
*
55462 TTTTTCTTTTTTCT
1 TTTTTCTTTTTCCT
*
55476 TTTTCCTTTTTCCT
1 TTTTTCTTTTTCCT
*
55490 TTTTTCATTTTCC-
1 TTTTTCTTTTTCCT
55503 TTTTTCTTT
1 TTTTTCTTT
55512 CTTCAGGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
13 8 0.26
14 23 0.74
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTTTCCT
Found at i:55491 original size:21 final size:21
Alignment explanation
Indices: 55446--55508 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
55436 TATTTTTTCA
* *
55446 TTCCTTTTTT-TCTTT-ATTT
1 TTCCTTTTTTCTTTTTCCTTT
55465 TT-CTTTTTTCTTTTTCCTTT
1 TTCCTTTTTTCTTTTTCCTTT
*
55485 TTCCTTTTTTCATTTTCCTTT
1 TTCCTTTTTTCTTTTTCCTTT
55506 TTC
1 TTC
55509 TTTCTTCAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 7 0.18
19 6 0.16
20 5 0.13
21 20 0.53
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (21 bp):
TTCCTTTTTTCTTTTTCCTTT
Found at i:61633 original size:20 final size:20
Alignment explanation
Indices: 61608--61657 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
61598 AAGAGTGTAC
61608 CGATGCACCAATCCATGCAT
1 CGATGCACCAATCCATGCAT
61628 CGATGCACCAATCCATGCAT
1 CGATGCACCAATCCATGCAT
61648 CGATGCACCA
1 CGATGCACCA
61658 TTGAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.36, G:0.16, T:0.18
Consensus pattern (20 bp):
CGATGCACCAATCCATGCAT
Found at i:61739 original size:65 final size:63
Alignment explanation
Indices: 61622--61827 Score: 186
Period size: 65 Copynumber: 3.2 Consensus size: 63
61612 GCACCAATCC
** * * ** *
61622 ATGCATCGATGCACCAATCCATGCATCGATGCAC-CATTGAATAAATTG-AACATAGAATGCCTT
1 ATGCATCGATGCA-CAAGACATGCATCGATGCACTCA-AG-CTATTTTGAAACATCGAATGCCTT
61685 AT
63 -T
* * * *
61687 ATGCATCGATGCACATA-CCATGTATCGATGCACTCAAG-TTTTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACA-AGACATGCATCGATGCACTCAAGCTATTT-TG-AAACATCGAATGCCTT
61750 T
63 T
* *
61751 GATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTTC
1 -ATGCATCGATGCACAAGACATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGC-CTTT
61816 ATGCATCGATGC
1 ATGCATCGATGC
61828 GCTCTTAGTG
Statistics
Matches: 119, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 45 0.38
65 66 0.55
66 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAAGACATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGCCTTT
Found at i:68908 original size:22 final size:22
Alignment explanation
Indices: 68883--68937 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
68873 CATTACCATT
68883 TAATTAAAAATTAATCAAGAGA
1 TAATTAAAAATTAATCAAGAGA
68905 TAATTAAAAATTAATCAAGAGA
1 TAATTAAAAATTAATCAAGAGA
68927 TAATTAAAAAT
1 TAATTAAAAAT
68938 GTGTTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (22 bp):
TAATTAAAAATTAATCAAGAGA
Found at i:69781 original size:7 final size:7
Alignment explanation
Indices: 69771--69813 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
69761 TTTTTCTTTA
69771 TTTTTCT
1 TTTTTCT
69778 TTTTTCT
1 TTTTTCT
*
69785 TTTTCCT
1 TTTTTCT
69792 TTTTTC-
1 TTTTTCT
* *
69798 ATTTTCA
1 TTTTTCT
69805 TTTTTCT
1 TTTTTCT
69812 TT
1 TT
69814 CTTAAGGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCT
Found at i:75959 original size:65 final size:63
Alignment explanation
Indices: 75890--76047 Score: 171
Period size: 65 Copynumber: 2.4 Consensus size: 63
75880 GAATAAATTG
* * *
75890 AACATCGAATGCCTTATACGCATCGATGCACATA-CCATGCATCGATGTACTCAGG-TTTTTATG
1 AACATCGAATGCCTTATA-GCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-TG
75953 AA
63 -A
*
75955 AACATCGAATGCATT-TGATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCCTTAT-A-GCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
*
76019 AACATCAAATGCACTTCAT-GCATCGATGC
1 AACATCGAATGC-CTT-ATAGCATCGATGC
76048 GCTCTTAGTG
Statistics
Matches: 80, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
64 24 0.30
65 51 0.64
66 4 0.05
67 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCCTTATAGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
Found at i:81924 original size:21 final size:22
Alignment explanation
Indices: 81900--81952 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
81890 CCTTTGAATA
81900 TGCATCGAT-ACACCATGAAGG
1 TGCATCGATCACACCATGAAGG
* * * *
81921 TGCACCGATGCACTCCTTGAATG
1 TGCATCGAT-CACACCATGAAGG
81944 TGCATCGAT
1 TGCATCGAT
81953 GCATCCGTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 8 0.32
23 17 0.68
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (22 bp):
TGCATCGATCACACCATGAAGG
Found at i:83523 original size:27 final size:27
Alignment explanation
Indices: 83493--83544 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
83483 AGGAGCGAGT
*
83493 TCTTCACGAGCACCTCCTGCTCCTAGC
1 TCTTCACGAGCACCTCCTCCTCCTAGC
* * *
83520 TCTTCTCGTGCTCCTCCTCCTCCTA
1 TCTTCACGAGCACCTCCTCCTCCTA
83545 CTCCGGCATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.10, C:0.46, G:0.12, T:0.33
Consensus pattern (27 bp):
TCTTCACGAGCACCTCCTCCTCCTAGC
Found at i:84823 original size:17 final size:19
Alignment explanation
Indices: 84801--84843 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
84791 GGAACATTAA
*
84801 ATGCACT-TCA-TGCATCG
1 ATGCACTCTCAGTGCACCG
*
84818 ATGCACTCTTAGTGCACCG
1 ATGCACTCTCAGTGCACCG
84837 ATGCACT
1 ATGCACT
84844 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (19 bp):
ATGCACTCTCAGTGCACCG
Found at i:86779 original size:29 final size:30
Alignment explanation
Indices: 86725--86783 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
86715 AATGAAATTA
86725 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
86755 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
86784 TTACAGCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Found at i:88020 original size:3 final size:3
Alignment explanation
Indices: 88014--88082 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
88004 TAATTATTTG
* *
88014 ATA ATA AT- ATA AT- ATGT ATA AT- ATA ATA ATA ATA TATT ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* *
88058 ATA ATA ATA ATT TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
88083 ATTTAAGTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
2 6 0.11
3 44 0.81
4 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:88039 original size:22 final size:22
Alignment explanation
Indices: 88015--88082 Score: 83
Period size: 21 Copynumber: 3.3 Consensus size: 22
88005 AATTATTTGA
*
88015 TAATAAT-ATAATAT-GTATAA
1 TAATAATAATAATATATTATAA
88035 T-ATAATAATAATATATTATAA
1 TAATAATAATAATATATTATAA
88056 TAATAATAATAAT-T-TTAATAA
1 TAATAATAATAATATATT-ATAA
88077 TAATAA
1 TAATAA
88083 ATTTAAGTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
19 5 0.12
20 10 0.23
21 17 0.40
22 11 0.26
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
TAATAATAATAATATATTATAA
Found at i:88048 original size:25 final size:25
Alignment explanation
Indices: 88014--88068 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
88004 TAATTATTTG
*
88014 ATAATAATATAATATGTATAAT-ATA
1 ATAATAATATAATAT-AATAATAATA
*
88039 ATAATAATATATTATAATAATAATA
1 ATAATAATATAATATAATAATAATA
88064 ATAAT
1 ATAAT
88069 TTTAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATAATAATATAATATAATAATAATA
Found at i:88361 original size:76 final size:76
Alignment explanation
Indices: 88241--88498 Score: 435
Period size: 76 Copynumber: 3.4 Consensus size: 76
88231 GAGGTCTTAA
* * * * * *
88241 AAACATCATGCACTGAAGGGCTTACAGATTACCCAAAGGTTTTGAAAACATCATAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
88306 AGGCTTTTTGG
66 AGGCTTTTTGG
*
88317 AAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
88382 ATGCTTTTTGG
66 AGGCTTTTTGG
*
88393 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCCA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
88458 AGGCTTTTTGG
66 AGGCTTTTTGG
88469 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
88499 TGGGAAATAG
Statistics
Matches: 171, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 171 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:88849 original size:76 final size:76
Alignment explanation
Indices: 88622--88983 Score: 604
Period size: 76 Copynumber: 4.8 Consensus size: 76
88612 TCAAAATAAC
* *
88622 AACACCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
88687 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
88698 AACATCAAAAAGCTCCCGAAGGCTTTTTGGGAAACAACATTCACTGTAGGACTTACAGATGACCC
1 AACATCAAAAAGCTCCCGAAGGCTTTTT-GGAAACATCATGCACTGTAGGACTTACAGATGACCC
*
88763 TAAGGTTTTGAA
65 TAAGGCTTTGAA
88775 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
88840 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
88851 AACATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCATGCACTGTAGGACTTACAGATCACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
88916 AAGGCTTTG-A
66 AAGGCTTTGAA
* * *
88926 AACATC-AAAATCTCCCGAAGGC-TTTTGAAAACATCATGCACTGTAGGAATTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
88984 TGGGAAATAG
Statistics
Matches: 270, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
73 33 0.12
74 14 0.05
75 7 0.03
76 144 0.53
77 72 0.27
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAA
Done.