Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000817.1 Hibiscus syriacus cultivar Beakdansim tig00001581_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: 86237
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:11188 original size:21 final size:20
Alignment explanation
Indices: 11159--11199 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
11149 TGATTATTAA
11159 AATTTATAAAATTATCTTAT
1 AATTTATAAAATTATCTTAT
* *
11179 AATTATATAATATTATTTTAT
1 AATT-TATAAAATTATCTTAT
11200 TAAATCACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTATAAAATTATCTTAT
Found at i:19929 original size:21 final size:21
Alignment explanation
Indices: 19900--19952 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19890 ATTCTGACTA
19900 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
19921 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
19942 TCGCAATGCGA
1 TCGCATTGCGA
19953 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:19967 original size:20 final size:20
Alignment explanation
Indices: 19942--20075 Score: 187
Period size: 20 Copynumber: 6.7 Consensus size: 20
19932 TTTTCCTAAT
19942 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
19962 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
19983 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
20003 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
20023 TTGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
20043 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
20063 TCGCAACGCGAAT
1 TCGCAATGCGAAT
20076 CTGACTATCG
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 83 0.85
21 15 0.15
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:20085 original size:20 final size:20
Alignment explanation
Indices: 20062--20128 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
20052 GAATACGTAA
* *
20062 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
* *
20082 ATCGCAGCAAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
20102 ATCGCAACGAGATTATGACT
1 ATCGCAACGAGATTCTGACT
20122 ATCGCAA
1 ATCGCAA
20129 TACTAAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:21022 original size:24 final size:24
Alignment explanation
Indices: 20971--21024 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
20961 GTATTCGAAA
*
20971 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
20995 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
21019 TTTGAT
1 TTTGAT
21025 GATTTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:23463 original size:20 final size:20
Alignment explanation
Indices: 23438--23531 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
23428 GACATTCATT
23438 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCAGAA-A
* *
23458 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCAGAAA
*
23478 TGACTATCGCAACGCAGAAT
1 TGACTATCGCAACGCAGAAA
*
23498 TGACTATCGCAACGCTGAAA
1 TGACTATCGCAACGCAGAAA
*
23518 TGACTATCACAACG
1 TGACTATCGCAACG
23532 AGAGAATCGC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 63 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCAGAAA
Found at i:23502 original size:40 final size:40
Alignment explanation
Indices: 23438--23531 Score: 145
Period size: 40 Copynumber: 2.4 Consensus size: 40
23428 GACATTCATT
23438 TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
* *
23478 TGACTATCGCAACGCAGAAT-TGACTATCGCAACGCTGAAA
1 TGACTATCGCAACGC-GAATATGACTATCGCAACACGGAAA
*
23518 TGACTATCACAACG
1 TGACTATCGCAACG
23532 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 46 0.92
41 4 0.08
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (40 bp):
TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
Found at i:23553 original size:33 final size:33
Alignment explanation
Indices: 23503--23633 Score: 154
Period size: 34 Copynumber: 3.8 Consensus size: 33
23493 AGAATTGACT
* ** * *
23503 ATCGCAACGCTGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGTGA
23537 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
* *
23570 ATTGCAATGCGAAAATGAAAATTGCAACGAGTGA
1 ATCGCAATGCG-AAATGAAAATCGCAACGAGTGA
*
23604 ATCGCAATGCGAAAATAAAAAATCGCAACG
1 ATCGCAATGCG-AAAT-GAAAATCGCAACG
23634 CGAATTTAGT
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.34
34 45 0.53
35 11 0.13
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
Found at i:23591 original size:34 final size:34
Alignment explanation
Indices: 23527--23633 Score: 162
Period size: 34 Copynumber: 3.1 Consensus size: 34
23517 ATGACTATCA
*
23527 CAACGAGAGAATCGCAATGCG-AAATGAAAATCG
1 CAACGAGTGAATCGCAATGCGAAAATGAAAATCG
* *
23560 CAACGAGTGAATTGCAATGCGAAAATGAAAATTG
1 CAACGAGTGAATCGCAATGCGAAAATGAAAATCG
*
23594 CAACGAGTGAATCGCAATGCGAAAATAAAAAATCG
1 CAACGAGTGAATCGCAATGCGAAAAT-GAAAATCG
23629 CAACG
1 CAACG
23634 CGAATTTAGT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 19 0.29
34 36 0.55
35 11 0.17
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (34 bp):
CAACGAGTGAATCGCAATGCGAAAATGAAAATCG
Found at i:23660 original size:14 final size:14
Alignment explanation
Indices: 23661--23694 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
23651 TGCGATTTTC
23661 ATTTTCGCATTGCG
1 ATTTTCGCATTGCG
* *
23675 ATTTTCTCGTTGCG
1 ATTTTCGCATTGCG
23689 ATTTTC
1 ATTTTC
23695 ATTTCGCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.50
Consensus pattern (14 bp):
ATTTTCGCATTGCG
Found at i:23668 original size:20 final size:19
Alignment explanation
Indices: 23643--23710 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 19
23633 GCGAATTTAG
*
23643 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
23662 TTTTCGCATTGCGATTTTC-
1 -TTTCGCATTGCGATTTTCA
23681 --TCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
23696 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
23711 CTCTCGTTGC
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
14 11 0.26
16 3 0.07
17 3 0.07
19 8 0.19
20 17 0.40
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.49
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:23705 original size:33 final size:33
Alignment explanation
Indices: 23643--23743 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 33
23633 GCGAATTTAG
*
23643 TTTCGCGTTGCGATTTTCATTTTCGCATTGCGAT
1 TTTCTCGTTGCGATTTTCA-TTTCGCATTGCGAT
23677 TTTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TTTCTCGTTGCGATTTTCATTTCGCATTGCGAT
* ** *
23710 TCTCTCGTTGCGATAGTCATTTCCGCGTTGCGAT
1 TTTCTCGTTGCGATTTTCATTT-CGCATTGCGAT
23744 AGTCTGTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 33 0.54
34 28 0.46
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTTCTCGTTGCGATTTTCATTTCGCATTGCGAT
Found at i:23868 original size:14 final size:14
Alignment explanation
Indices: 23849--23885 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
23839 CATCAATTAA
23849 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
23863 ACAAATCATCTTTT
1 ACAAATCAACATTT
23877 ACAAATCAA
1 ACAAATCAA
23886 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:25348 original size:21 final size:21
Alignment explanation
Indices: 25300--25357 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
25290 TGATGACAGT
* *
25300 GGCCTCTTGAACGGTGGGAGG
1 GGCCTCTTGAACGATGGGAGA
*
25321 GGACTCTTGAACGATAGGG-GA
1 GGCCTCTTGAACGAT-GGGAGA
25342 GGCCTCTTGAACGATG
1 GGCCTCTTGAACGATG
25358 ACAGGTAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.88
22 3 0.09
ACGTcount: A:0.21, C:0.19, G:0.40, T:0.21
Consensus pattern (21 bp):
GGCCTCTTGAACGATGGGAGA
Found at i:25865 original size:20 final size:20
Alignment explanation
Indices: 25842--25970 Score: 186
Period size: 20 Copynumber: 6.5 Consensus size: 20
25832 GAAACTTAAA
*
25842 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
25862 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
25882 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
25902 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
25922 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* **
25942 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
25962 ATCGCAACG
1 ATCGCAACG
25971 AGAGAATCGC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:26040 original size:20 final size:20
Alignment explanation
Indices: 26015--26101 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
26005 GATTCTTTCG
**
26015 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCATTTTCACA
*
26035 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCACA
26055 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCACA
* *
26075 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCACA
26095 TTGCGAT
1 TTGCGAT
26102 TTTGTTGTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCACA
Found at i:26063 original size:40 final size:40
Alignment explanation
Indices: 26015--26101 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 40
26005 GATTCTTTCG
26015 TTGCGATAGTCAAATTCACATTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCACATTGCGATAGTCATTTTCGCA
** *
26055 TTGCGATAGTCATTTTCACATTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCACATTGCGATAGTCATTTTCGCA
26095 TTGCGAT
1 TTGCGAT
26102 TTTGTTGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCACATTGCGATAGTCATTTTCGCA
Found at i:26167 original size:20 final size:20
Alignment explanation
Indices: 26140--26191 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
26130 GCGATTCTCT
26140 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
26160 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
26180 CATTGCGATAGT
1 CATTGCGATAGT
26192 AAACTATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:28085 original size:20 final size:20
Alignment explanation
Indices: 28062--28151 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
28052 TCTGAAACTT
28062 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
28082 AAAATCGCAACACAAAAATG
1 AAAATCGCAACACGAAAATG
** * * **
28102 ACTATCACAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
28122 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
28141 AAAATCGCAAC
1 AAAATCGCAAC
28152 GACATAATCA
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
19 12 0.21
20 45 0.79
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:28761 original size:20 final size:20
Alignment explanation
Indices: 28738--28820 Score: 103
Period size: 20 Copynumber: 4.1 Consensus size: 20
28728 TTCACGTTGA
28738 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
*
28758 GATTTACGTAATCGCATTGC
1 GATTTACGTATTCGCATTGC
* ** *
28778 GATTTTCCAAATTCGCGTTGC
1 GA-TTTACGTATTCGCATTGC
*
28799 AATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
28819 GA
1 GA
28821 ATTAGGAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 36 0.72
21 14 0.28
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
GATTTACGTATTCGCATTGC
Found at i:28834 original size:21 final size:21
Alignment explanation
Indices: 28810--28862 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
28800 ATTTACGTAT
*
28810 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
28831 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
28852 TCGCAATGCGA
1 TCGCAATGCGA
28863 TAGTCAGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:40663 original size:5 final size:5
Alignment explanation
Indices: 40634--40688 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
40624 TAAACTTAAT
40634 TAAAA -AAACA TAAAA -AAACA TAAAA TAAAA TAAAA TAAAA TAAAA CTAAATA
1 TAAAA TAAA-A TAAAA TAAA-A TAAAA TAAAA TAAAA TAAAA TAAAA -TAAA-A
40686 TAA
1 TAA
40689 GGACCTAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
4 6 0.14
5 24 0.55
6 13 0.30
7 1 0.02
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:42329 original size:23 final size:23
Alignment explanation
Indices: 42301--42375 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
42291 GACAACACAG
* **
42301 AAAAGAAAGAAAGAGAAAATTAA
1 AAAAGAAAGAAAAAGAAAAGAAA
42324 AAAAGAAAGAAAAAGAAAAGAAA
1 AAAAGAAAGAAAAAGAAAAGAAA
42347 AAAAG-AAGAAGAAA-AAAAG-AA
1 AAAAGAAAGAA-AAAGAAAAGAAA
*
42368 GAAAGAAA
1 AAAAGAAA
42376 ACAAACACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 6 0.13
22 12 0.26
23 28 0.61
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.03
Consensus pattern (23 bp):
AAAAGAAAGAAAAAGAAAAGAAA
Found at i:42343 original size:11 final size:11
Alignment explanation
Indices: 42301--42376 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
42291 GACAACACAG
42301 AAAAG-AAAGA
1 AAAAGAAAAGA
* *
42311 AAGAGAAAATTA
1 AAAAGAAAA-GA
42323 AAAA-AGAAAGA
1 AAAAGA-AAAGA
42334 AAAAGAAAAGA
1 AAAAGAAAAGA
42345 AAAA-AAGAAGA
1 AAAAGAA-AAGA
42356 AGAAA-AAAAGA
1 A-AAAGAAAAGA
42367 AGAAAGAAAA
1 A-AAAGAAAA
42377 CAAACACTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
10 6 0.11
11 32 0.58
12 17 0.31
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:42358 original size:14 final size:14
Alignment explanation
Indices: 42333--42376 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
42323 AAAAAGAAAG
42333 AAAAAGAA-AAGAA
1 AAAAAGAAGAAGAA
42346 AAAAAGAAGAAGAA
1 AAAAAGAAGAAGAA
42360 AAAAAGAAGAAAGAA
1 AAAAAGAAG-AAGAA
42375 AA
1 AA
42377 CAAACACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.28
14 14 0.48
15 7 0.24
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGAAGAA
Found at i:44846 original size:39 final size:39
Alignment explanation
Indices: 44796--45017 Score: 351
Period size: 39 Copynumber: 5.7 Consensus size: 39
44786 AGAAGAACTT
*
44796 GAAACATAAGATTTTATCTCGCTTGAGATAGTTTCACTC
1 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTC
* *
44835 GAAAAAGAAGATTTTATCTCGCTTAAGATAGTTTCACTC
1 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTC
44874 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTC
1 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTC
* * *
44913 GAAACATAAGA-TTCATCTTGCTTGAGATAGTTTCACTC
1 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTC
*
44951 GAAACATAAGATTTTATCTCGCTTGAGATAGTTTCACTC
1 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTC
44990 GAAACAGAAGA-TTTATCTCAG-TTGAGAT
1 GAAACAGAAGATTTTATCTC-GCTTGAGAT
45018 TATTTTTCTT
Statistics
Matches: 170, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
38 51 0.30
39 119 0.70
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (39 bp):
GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTC
Found at i:44962 original size:22 final size:22
Alignment explanation
Indices: 44937--45001 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
44927 ATCTTGCTTG
44937 AGATAGTTTCACTCGAAACATA
1 AGATAGTTTCACTCGAAACATA
* *
44959 AGAT--TTT-ATCTCG---CTTG
1 AGATAGTTTCA-CTCGAAACATA
*
44976 AGATAGTTTCACTCGAAACAGA
1 AGATAGTTTCACTCGAAACATA
44998 AGAT
1 AGAT
45002 TTATCTCAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 14
0.62 0.10 0.28
Matches are distributed among these distances:
17 6 0.19
19 8 0.26
20 8 0.26
22 9 0.29
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (22 bp):
AGATAGTTTCACTCGAAACATA
Found at i:45033 original size:77 final size:77
Alignment explanation
Indices: 44796--45017 Score: 365
Period size: 77 Copynumber: 2.9 Consensus size: 77
44786 AGAAGAACTT
* *
44796 GAAACATAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTTTATCTCGCTTAA
1 GAAACATAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCTCGCTTGA
44861 GATAGTTTCACTC
65 GATAGTTTCACTC
* * * *
44874 GAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACATAAGATTCATCTTGCTTGAG
1 GAAACATAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCGCTTGAG
44939 ATAGTTTCACTC
66 ATAGTTTCACTC
44951 GAAACATAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCAG-TTGA
1 GAAACATAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTC-GCTTGA
45015 GAT
65 GAT
45018 TATTTTTCTT
Statistics
Matches: 133, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
77 85 0.64
78 48 0.36
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (77 bp):
GAAACATAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCGCTTGAG
ATAGTTTCACTC
Found at i:45290 original size:136 final size:136
Alignment explanation
Indices: 45040--45421 Score: 548
Period size: 136 Copynumber: 2.8 Consensus size: 136
45030 AACAAACTAT
* * * * * * * * *
45040 GCCTTGCTTGAGGGATTAACATTTCCGATGGAGAATTTATAATGATAAGAACTCATCCGATAGAG
1 GCCTCGCTTGAGAGAATGACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAG
* * *
45105 GGAGAAGAAGTTCATAATGAGAAGAAATTGTTCGACCTATTGCTTGATTCACAACACTTTAAATC
66 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACAACACTTCAAATC
45170 AGCAAC
131 AGCAAC
* * *
45176 GCCTCGCTTGAGAGAATGATATTTTCGATGGAGAGTTGATAATGAGAAGAACGCATCCGACAGAG
1 GCCTCGCTTGAGAGAATGACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAG
*
45241 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACAACACTTCGAATC
66 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACAACACTTCAAATC
*
45306 AGCAAT
131 AGCAAC
* * * * *
45312 GCCTCGCTTGAGGGATTGACATTTTCGATAGAGAGTTCATAATGAGATGAACTCATCTGACAGAG
1 GCCTCGCTTGAGAGAATGACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAG
* *
45377 AGAGAAGAAATTCATAATGAGAAGAACTTGTTCGACCTATTGCTC
66 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATTGCTC
45422 AACTGAGAGA
Statistics
Matches: 220, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
136 220 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (136 bp):
GCCTCGCTTGAGAGAATGACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAG
GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACAACACTTCAAATC
AGCAAC
Found at i:50871 original size:215 final size:215
Alignment explanation
Indices: 50484--50895 Score: 704
Period size: 215 Copynumber: 1.9 Consensus size: 215
50474 TTTGGGTTGA
*
50484 CAATTAGAGGGCGGTGCCGTACAGCTTCAACCATGCTAGCTTCTGCTTCAACCATGGCCTCAAGT
1 CAATTAGAGGGCGGTGCCGTAAAGCTTCAACCATGCTAGCTTCTGCTTCAACCATGGCCTCAAGT
50549 GATCCATAGTTCCGTGTCAATCCATCTAATCAATTGGACAGTCGAATTAATTTAGGATCGAGATG
66 GATCCATAGTTCCGTGTCAATCCATCTAATCAATTGGACAGTCGAATTAATTTAGGATCGAGATG
50614 TAACGTAAATCATGAAATTTATTATTATTATTTTTAGCTTGAATGCATATTTCCCCTGAACTATA
131 TAACGTAAATCATGAAATTTATTATTATTATTTTTAGCTTGAATGCATATTTCCCCTGAACTATA
50679 CCCGGTTGCCATTAAAGCAT
196 CCCGGTTGCCATTAAAGCAT
*
50699 CAATTAGAGGGCGGTGCCGTAAAGC-TGAATCCATGCTAGCTTCTGCTTCAACCATGGCCTCAAG
1 CAATTAGAGGGCGGTGCCGTAAAGCTTCAA-CCATGCTAGCTTCTGCTTCAACCATGGCCTCAAG
* *
50763 TGATCCA-AGTTCTGTTTCAATCCATCTAATCAATTGGACAGTCGAATTAATTTAGGATCGAGAT
65 TGATCCATAGTTCCGTGTCAATCCATCTAATCAATTGGACAGTCGAATTAATTTAGGATCGAGAT
* * * *
50827 GTAACGTAAATCATGAAATTTATT-TTAATTTGTTTTTGGCTTGAATGCATATTTCCCCTTAATT
130 GTAACGTAAATCATGAAATTTATTATT-A-TTATTTTTAGCTTGAATGCATATTTCCCCTGAACT
50891 ATACC
193 ATACC
50896 TTTTATACTG
Statistics
Matches: 186, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
213 2 0.01
214 83 0.45
215 101 0.54
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (215 bp):
CAATTAGAGGGCGGTGCCGTAAAGCTTCAACCATGCTAGCTTCTGCTTCAACCATGGCCTCAAGT
GATCCATAGTTCCGTGTCAATCCATCTAATCAATTGGACAGTCGAATTAATTTAGGATCGAGATG
TAACGTAAATCATGAAATTTATTATTATTATTTTTAGCTTGAATGCATATTTCCCCTGAACTATA
CCCGGTTGCCATTAAAGCAT
Found at i:51850 original size:26 final size:27
Alignment explanation
Indices: 51807--51857 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
51797 AACTTTGTTC
**
51807 GGTTCGGTTAATTATTAAAA-AAAATT
1 GGTTCGGTTAACGATTAAAACAAAATT
*
51833 GGTTCGGTTAACGGTTAAAACAAAA
1 GGTTCGGTTAACGATTAAAACAAAA
51858 AAAGTTTCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (27 bp):
GGTTCGGTTAACGATTAAAACAAAATT
Found at i:57722 original size:3 final size:3
Alignment explanation
Indices: 57714--57826 Score: 190
Period size: 3 Copynumber: 37.7 Consensus size: 3
57704 CCTGCAAATG
* * * *
57714 TAA TAA TAA TAA TAT TAA TAA TAG TAT TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57762 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57810 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
57827 TAAACCCAGA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:58306 original size:129 final size:129
Alignment explanation
Indices: 58162--58663 Score: 607
Period size: 129 Copynumber: 3.9 Consensus size: 129
58152 TTAACACGAT
* * * * * *
58162 TCCTACATAATGAGGAAATCTA-GTCGGGTGATGACACGTTTCCTACGTGATAAGGACGGCAGGC
1 TCCTACGTGATGAGGAAATC-AGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGC
* * * * *
58226 CATCTATAGATGATAACACAGTTCCTACATGATGAGGACGATTGGTTATCTGGGGTTGACACGGC
65 CATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCTGGGTTTGACACGGC
* * * * * *
58291 TCCTACTTGATGAGGAGATCAGGTC-AGGTGATGACACGGTACCTACGCGATGAGGAAGACTA-G
1 TCCTACGTGATGAGGAAATCAGGTCGA-GTGATGACACGGTTCCTACGTGATGAGGACGTC-AGG
* *
58354 CCATCTA-AGGGTGATAACACGGTTCCTACGTGATGAGGACGGTTAGTTATCTGGGTTTGACATG
64 CCATCTATA-GGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCTGGGTTTGACACG
58418 GC
128 GC
* * * * * * * *
58420 TCCTGCGTGATGAGGAGATCAGGTTGAGTGATGACAAGGTTCCTACATGATGAGGACATCAAGTC
1 TCCTACGTGATGAGGAAATCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGCC
** * *
58485 ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGTTTGACACAGC
66 ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCTGGGTTTGACACGGC
* ** * **
58549 TCCTACGTGATGAAGAAGCCAGGTTGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTT
1 TCCTACGTGATGAGGAAATCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGCC
58614 ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCT
66 ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCT
58664 AGAGTGACAA
Statistics
Matches: 321, Mismatches: 45, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
128 3 0.01
129 315 0.98
130 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (129 bp):
TCCTACGTGATGAGGAAATCAGGTCGAGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGCC
ATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGATTAGTTATCTGGGTTTGACACGGC
Found at i:58652 original size:46 final size:45
Alignment explanation
Indices: 58188--58652 Score: 253
Period size: 46 Copynumber: 10.7 Consensus size: 45
58178 AATCTAGTCG
* * * **
58188 GGTGATGACACGTTTCCTACGTGATAAGGACGGCAGGCCATCTATA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCT-TA
* * * * *
58234 GATGATAACACAGTTCCTACATGATGAGGACGAT-TGGTTATC-T-
1 GGTGATGACACGGTTCCTACGTGATGAGGACG-TCAGGTTATCTTA
* * * *
58277 GGGGTTGACACGGCTCCTACTTGATGAGGA-GATCAGG---TC--A
1 GGTGATGACACGGTTCCTACGTGATGAGGACG-TCAGGTTATCTTA
* * * * ** *
58317 GGTGATGACACGGTACCTACGCGATGAGGAAGACTA-GCCATCTAA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTC-AGGTTATCTTA
* * *
58362 GGGTGATAACACGGTTCCTACGTGATGAGGACGGTTA-GTTATC-TG
1 -GGTGATGACACGGTTCCTACGTGATGAGGAC-GTCAGGTTATCTTA
* * * * *
58407 GGT-TTGACATGGCTCCTGCGTGATGAGGA-GATCAGG---T-TGA
1 GGTGATGACACGGTTCCTACGTGATGAGGACG-TCAGGTTATCTTA
* * * * *
58447 -GTGATGACAAGGTTCCTACATGATGAGGACATCAAGTCATCTATA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCT-TA
* * * *
58492 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATC-TG
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCTTA
* * * * * * *
58536 GGT-TTGACACAGCTCCTACGTGATGAAGAAGCCAGG---T-TGA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCTTA
58576 -GTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCTATA
1 GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCT-TA
*
58621 GGTGATAACACGGTTCCTACGTGATGAGGACG
1 GGTGATGACACGGTTCCTACGTGATGAGGACG
58653 ATTAGTTATC
Statistics
Matches: 310, Mismatches: 78, Indels: 62
0.69 0.17 0.14
Matches are distributed among these distances:
39 4 0.01
40 82 0.26
41 3 0.01
42 5 0.02
43 76 0.25
44 10 0.03
45 3 0.01
46 126 0.41
47 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.25
Consensus pattern (45 bp):
GGTGATGACACGGTTCCTACGTGATGAGGACGTCAGGTTATCTTA
Found at i:58755 original size:32 final size:33
Alignment explanation
Indices: 58713--58798 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
58703 GCACAATAGT
* *
58713 CTTCTTCGTGAAGTTGAAATTGTG-GGTGG-CTC
1 CTTCGTCGTGAAGTTGAAATT-TGAGGTGGAATC
* *
58745 CTTCGTCGTGAAGTTGAACTTTGAGTTGGATATC
1 CTTCGTCGTGAAGTTGAAATTTGAGGTGGA-ATC
*
58779 CTTCGTTGTGAAGTTGAAAT
1 CTTCGTCGTGAAGTTGAAAT
58799 CCAATCTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.04
32 23 0.51
34 20 0.44
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (33 bp):
CTTCGTCGTGAAGTTGAAATTTGAGGTGGAATC
Found at i:60978 original size:52 final size:52
Alignment explanation
Indices: 60914--61036 Score: 160
Period size: 52 Copynumber: 2.4 Consensus size: 52
60904 GAGTGAGCCT
* * *
60914 TCAAGATGCCCCACATGGATTACTTCTGTATTTTTT-ATGCTGATGTGAACCC
1 TCAAGATACCCCACATGGATTACTTCTAT-TTTTTTCATGATGATGTGAACCC
* * *
60966 TCAAGATACCCCATATGGATTACTTCTATTTTTTTCATGATGATGTGAGCCT
1 TCAAGATACCCCACATGGATTACTTCTATTTTTTTCATGATGATGTGAACCC
*
61018 TCAAGATA-CCTACATGGAT
1 TCAAGATACCCCACATGGAT
61037 AATATGGACC
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
51 15 0.24
52 47 0.76
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (52 bp):
TCAAGATACCCCACATGGATTACTTCTATTTTTTTCATGATGATGTGAACCC
Found at i:62574 original size:5 final size:5
Alignment explanation
Indices: 62564--62668 Score: 80
Period size: 5 Copynumber: 20.8 Consensus size: 5
62554 TTATATCTTT
62564 TTTTC TTTTC TTTTC TTTTC -TTT- TTTTC TTTT- TTCTT- TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC
*
62611 TTTTTTC TTTTC -TTTC TTTTT TTCTCTC TTTTC TTTT- TTTCTC TATTT-
1 --TTTTC TTTTC TTTTC TTTTC TT-T-TC TTTTC TTTTC TTT-TC T-TTTC
62659 TCTTTC TTTT
1 T-TTTC TTTT
62669 TTTATAGATG
Statistics
Matches: 84, Mismatches: 3, Indels: 26
0.74 0.03 0.23
Matches are distributed among these distances:
4 17 0.20
5 52 0.62
6 5 0.06
7 10 0.12
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:62590 original size:26 final size:25
Alignment explanation
Indices: 62561--62671 Score: 100
Period size: 27 Copynumber: 4.4 Consensus size: 25
62551 TTTTTATATC
*
62561 TTTTTTTCTTTTCTTTTCTTTTCTT
1 TTTTTTTTTTTTCTTTTCTTTTCTT
*
62586 TTTTTCTTTTTTCTTTTTTCTTTTCTT
1 TTTTT-TTTTTT-TCTTTTCTTTTCTT
* *
62613 TTTTCTTTTCTTTCTTTT-TTTCTCTC
1 TTTT-TTTTTTTTCTTTTCTTT-TCTT
* * *
62639 TTTTCTTTTTTTC-TCTATTTTCTT
1 TTTTTTTTTTTTCTTTTCTTTTCTT
*
62663 TCTTTTTTT
1 TTTTTTTTT
62672 ATAGATGAGT
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
24 12 0.17
25 18 0.26
26 17 0.24
27 22 0.31
28 1 0.01
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTTTTTTTTTCTTTTCTTTTCTT
Found at i:62613 original size:62 final size:61
Alignment explanation
Indices: 62533--62671 Score: 167
Period size: 62 Copynumber: 2.2 Consensus size: 61
62523 CTTGATTCAA
* * *
62533 TTTCTTTTTTTATATCTTTTTT-TATATCTTTTTTTCTTTTCTTTTCTTTTCTTTTTTTCT-T-T
1 TTTCTTTTTTT-TTTCTTTTTTCT-TATCTTTCTTT-TTTTC-TCTCTTTTCTTTTTTTCTCTAT
*
62595 TTTCTTTTTTCTTTTCTTTTTTCTTTTCTTTCTTTTTTTCTCTCTTTTCTTTTTTTCTCTAT
1 TTTCTTTTTT-TTTTCTTTTTTCTTATCTTTCTTTTTTTCTCTCTTTTCTTTTTTTCTCTAT
62657 TTTCTTTCTTTTTTT
1 TTTCTTT-TTTTTTT
62672 ATAGATGAGT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
60 17 0.25
61 6 0.09
62 40 0.59
63 5 0.07
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81
Consensus pattern (61 bp):
TTTCTTTTTTTTTTCTTTTTTCTTATCTTTCTTTTTTTCTCTCTTTTCTTTTTTTCTCTAT
Found at i:62650 original size:17 final size:16
Alignment explanation
Indices: 62533--62668 Score: 108
Period size: 17 Copynumber: 8.7 Consensus size: 16
62523 CTTGATTCAA
*
62533 TTTCTTTTTTTATATCT
1 TTTCTTTTTTTCT-TCT
* * *
62550 TTT-TTTATATCTTTT
1 TTTCTTTTTTTCTTCT
*
62565 TTTCTTTTCTT-TTCT
1 TTTCTTTTTTTCTTCT
62580 TTTCTTTTTTTCTT-T
1 TTTCTTTTTTTCTTCT
62595 TTTC---TTTT-TTCT
1 TTTCTTTTTTTCTTCT
*
62607 TTTC-TTTTTTCTTTT
1 TTTCTTTTTTTCTTCT
62622 CTTTCTTTTTTTCTCTCT
1 -TTTCTTTTTTTCT-TCT
*
62640 TTTCTTTTTTTCTCTAT
1 TTTCTTTTTTTCT-TCT
62657 TTTCTTTCTTTT
1 TTTCTTT-TTTT
62669 TTTATAGATG
Statistics
Matches: 97, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
11 2 0.02
12 9 0.09
14 4 0.04
15 26 0.27
16 16 0.16
17 34 0.35
18 6 0.06
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTTTCTTCT
Found at i:62660 original size:38 final size:34
Alignment explanation
Indices: 62561--62671 Score: 122
Period size: 38 Copynumber: 3.1 Consensus size: 34
62551 TTTTTATATC
62561 TTTTTTTCTTTTCTTTTCTTTTCTTTTTTTCTTT-TT
1 TTTTTTTCTTTTCTTTT-TTTTC--TTTTTCTTTCTT
62597 TCTTTTTTCTTTTC--TTTTTTC-TTTTCTTTCTT
1 T-TTTTTTCTTTTCTTTTTTTTCTTTTTCTTTCTT
62629 TTTTTCTCTCTTTTCTTTTTTTCTCTATTTTCTTTCTT
1 TTTTT-T-TCTTTTCTTTTTTT-TCT-TTTTCTTTCTT
62667 TTTTT
1 TTTTT
62672 ATAGATGAGT
Statistics
Matches: 66, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
31 12 0.18
32 4 0.06
33 7 0.11
34 5 0.08
35 7 0.11
36 3 0.05
37 12 0.18
38 16 0.24
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (34 bp):
TTTTTTTCTTTTCTTTTTTTTCTTTTTCTTTCTT
Found at i:62671 original size:12 final size:12
Alignment explanation
Indices: 62533--62671 Score: 105
Period size: 12 Copynumber: 11.9 Consensus size: 12
62523 CTTGATTCAA
*
62533 TTTCTTTTTTTA
1 TTTCTTTTTTTC
* *
62545 TATCTTTTTTTA
1 TTTCTTTTTTTC
*
62557 TATCTTTTTTTC
1 TTTCTTTTTTTC
*
62569 -TT-TTCTTTTC
1 TTTCTTTTTTTC
*
62579 -TT-TTCTTTT-
1 TTTCTTTTTTTC
62588 TTTC-TTTTTTC
1 TTTCTTTTTTTC
62599 TTT-TTTCTTTTC
1 TTTCTTT-TTTTC
62611 TTT-TTTCTTTTC
1 TTTCTTT-TTTTC
62623 TTTCTTTTTTTC
1 TTTCTTTTTTTC
* *
62635 TCTCTTTTCTTTT
1 TTTCTTTT-TTTC
*
62648 TTTCTCTATTTTC
1 TTTCT-TTTTTTC
62661 TTTCTTTTTTT
1 TTTCTTTTTTT
62672 ATAGATGAGT
Statistics
Matches: 108, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
10 23 0.21
11 6 0.06
12 59 0.55
13 18 0.17
14 2 0.02
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:68789 original size:3 final size:3
Alignment explanation
Indices: 68781--68866 Score: 136
Period size: 3 Copynumber: 28.7 Consensus size: 3
68771 CCTGCAAATG
* * * *
68781 TAA TAA TAA TAA TAT TAA TAA TAG TAT TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
68829 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
68867 TAAACCCGGA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:71386 original size:6 final size:6
Alignment explanation
Indices: 71375--71869 Score: 886
Period size: 6 Copynumber: 84.0 Consensus size: 6
71365 TAAAATTAGA
71375 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
71423 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
71471 ATGTAT ATGTAT ATGTAT ATG--T ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
71517 ATGT-T ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
71564 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
71612 ATGTAT ATGTAT ATGTAT ATG--T ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
71658 ATGTATAT ATGTAT ATGTAT ATGTAT ATGTAT A-GTAT ATGTAT ATGTAT
1 ATG--TAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
71707 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
71755 ATG--T ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG--T
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
71799 ATGTAT ATGTAT ATGTAT A-GTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
*
71846 ATGTAT ATGTAT ATGTAT ACGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT
71870 TCATGTGGAC
Statistics
Matches: 475, Mismatches: 1, Indels: 26
0.95 0.00 0.05
Matches are distributed among these distances:
4 16 0.03
5 15 0.03
6 438 0.92
8 6 0.01
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATGTAT
Done.