Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1205
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: 37246
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:70 original size:13 final size:13
Alignment explanation
Indices: 52--138 Score: 84
Period size: 13 Copynumber: 7.3 Consensus size: 13
42 ACATTATGCT
52 TTGTATCGATACA
1 TTGTATCGATACA
65 TTGTATCGATACA
1 TTGTATCGATACA
*
78 -TGT-TC-AGCACA
1 TTGTATCGA-TACA
89 TTGTATCGATACA
1 TTGTATCGATACA
*
102 ATGTATCGATACA
1 TTGTATCGATACA
115 -TG-AT-G--A-A
1 TTGTATCGATACA
122 TTGTATCGATACA
1 TTGTATCGATACA
135 TTGT
1 TTGT
139 TTCTAACGGC
Statistics
Matches: 61, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
7 1 0.02
8 3 0.05
9 2 0.03
10 3 0.05
11 7 0.11
12 9 0.15
13 35 0.57
14 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:73 original size:33 final size:33
Alignment explanation
Indices: 31--138 Score: 128
Period size: 33 Copynumber: 3.2 Consensus size: 33
21 ACACACCCAA
*
31 ATTGTATCGATACATTATGCTTTGTATCGATAC
1 ATTGTATCGATACATTATGCATTGTATCGATAC
64 ATTGTATCGATACATGT-TCAGCACATTGTATCGATAC
1 ATTGTATCGATACAT-TAT--G--CATTGTATCGATAC
* * *
101 AATGTATCGATACATGATGAATTGTATCGATAC
1 ATTGTATCGATACATTATGCATTGTATCGATAC
134 ATTGT
1 ATTGT
139 TTCTAACGGC
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
33 33 0.52
34 1 0.02
35 2 0.03
37 28 0.44
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (33 bp):
ATTGTATCGATACATTATGCATTGTATCGATAC
Found at i:1544 original size:38 final size:34
Alignment explanation
Indices: 1487--1574 Score: 97
Period size: 38 Copynumber: 2.4 Consensus size: 34
1477 ATCAAAATTT
**
1487 TATATAATATTTAATTGATTAAAATTTATATAAAA
1 TATATAATATTTAATTGATTAAAATAAATA-AAAA
1522 TATATAATATTTAAAATATGATTAAAATAAATAAAAA
1 TATATAATATTT--AAT-TGATTAAAATAAATAAAAA
1559 TAATATAA-ATTATAAT
1 T-ATATAATATT-TAAT
1575 ATAAATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
35 12 0.26
36 3 0.07
37 11 0.24
38 20 0.43
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (34 bp):
TATATAATATTTAATTGATTAAAATAAATAAAAA
Found at i:3928 original size:26 final size:27
Alignment explanation
Indices: 3860--3929 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
3850 GAAATGGTCA
*
3860 TCAAGAAATTATCGTCAAGAACTTCTG
1 TCAAGAAATTTTCGTCAAGAACTTCTG
* *
3887 TCGAG-AATGTTT-GTCAGGAACTT-TG
1 TCAAGAAAT-TTTCGTCAAGAACTTCTG
3912 TCAAGAAATTTTCGTCAA
1 TCAAGAAATTTTCGTCAA
3930 TACGAAAGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 9 0.26
26 20 0.57
27 6 0.17
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (27 bp):
TCAAGAAATTTTCGTCAAGAACTTCTG
Found at i:4087 original size:30 final size:30
Alignment explanation
Indices: 3934--4468 Score: 466
Period size: 28 Copynumber: 18.1 Consensus size: 30
3924 CGTCAATACG
* *
3934 AAAGCCCACAAGTCAGTGGC-ATCCTTCTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
* * **
3963 ATAGCCCACAAGTCAATGGC-A-TTTTTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
* *
3991 AAAGCCCATAAGTCAGTGGC-ATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
* *
4019 AAAGCCCACAAGTTAGTGGC-ATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
* *
4047 AAAGTCCACAAGTCAATGGCATACCCTTTT-
1 AAAGCCCACAAGTCAGTGGCA-ACCCTTTTC
*
4077 AAAGCTCACAAGTCAGTGGC-ACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
* **
4106 AAAGCCCACAAGTCAGTGGTAATTCTTTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
*
4136 AAAGTCCACACAAGTCGGTGGC-ACCC-TTTC
1 AAAG-CC-CACAAGTCAGTGGCAACCCTTTTC
* *
4166 AAAGCCCATAAGTCTGTGGC-ACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
** *
4195 AAAGCCCACAAGTCAGTGATAACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
** *
4225 AAAGTCCACACAAGTTGGTAGC-ACCCTTTT-
1 AAAG-CC-CACAAGTCAGTGGCAACCCTTTTC
4255 AAAGCCCACAAGTCAGTGGC-ACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
* *
4284 AAAGCCCACAAGTCAGTGGTAACTCTTTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
* *
4314 AAAGTCCACACAAGTCGGTGGCAA-CTTTGTTC
1 AAAG-CC-CACAAGTCAGTGGCAACCCTT-TTC
* *
4346 AAAGCCCACACAAGTCAATGG-TACCC-TTTC
1 AAAG-CC-CACAAGTCAGTGGCAACCCTTTTC
4376 AAAGCCCACAAGTCAGTGGCACACCC-TTTC
1 AAAGCCCACAAGTCAGTGGCA-ACCCTTTTC
* * *
4406 AAAGCTCTCAAGTCGGTGGC-ACCC-TTTC
1 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
* *
4434 AAAGCCCATACAAGTC-GATGACAACTCTTTTC
1 AAAGCCC--ACAAGTCAG-TGGCAACCCTTTTC
4466 AAA
1 AAA
4469 TCACCACTTT
Statistics
Matches: 418, Mismatches: 63, Indels: 47
0.79 0.12 0.09
Matches are distributed among these distances:
28 138 0.33
29 83 0.20
30 108 0.26
31 25 0.06
32 64 0.15
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCAACCCTTTTC
Found at i:4170 original size:89 final size:88
Alignment explanation
Indices: 3934--4441 Score: 559
Period size: 89 Copynumber: 5.8 Consensus size: 88
3924 CGTCAATACG
* * * ** ***
3934 AAAGCCCACAAGTCAGTGG-CATCCTTCTCATAG-CC-CACAAGTCAATGGCATTTTTTCAAAGC
1 AAAGCCCACAAGTCAGTGGTAAT-CTTTTCAAAGTCCACACAAGTCGGTGGCACCCTTTCAAAGC
* *
3996 CCATAAGTCAGTGGCATCC-TTTC
65 CCACAAGTCAGTGGCACCCTTTTC
* * * ** *
4019 AAAGCCCACAAGTTAGTGG-CATCCTTTCAAAGT-C-CACAAGTCAATGGCATACCCTTTTAAAG
1 AAAGCCCACAAGTCAGTGGTAATCTTTTCAAAGTCCACACAAGTCGGTGGC--ACCCTTTCAAAG
*
4081 CTCACAAGTCAGTGGCACCCTTTTC
64 CCCACAAGTCAGTGGCACCCTTTTC
4106 AAAGCCCACAAGTCAGTGGTAATTCTTTTCAAAGTCCACACAAGTCGGTGGCACCCTTTCAAAGC
1 AAAGCCCACAAGTCAGTGGTAA-TCTTTTCAAAGTCCACACAAGTCGGTGGCACCCTTTCAAAGC
* *
4171 CCATAAGTCTGTGGCACCCTTTTC
65 CCACAAGTCAGTGGCACCCTTTTC
* * * *
4195 AAAGCCCACAAGTCAGTGATAACTCTTTTCAAAGTCCACACAAGTTGGTAGCACCCTTTTAAAGC
1 AAAGCCCACAAGTCAGTGGTAA-TCTTTTCAAAGTCCACACAAGTCGGTGGCACCCTTTCAAAGC
4260 CCACAAGTCAGTGGCACCCTTTTC
65 CCACAAGTCAGTGGCACCCTTTTC
**
4284 AAAGCCCACAAGTCAGTGGTAACTCTTTTCAAAGTCCACACAAGTCGGTGGCAACTTTGTTCAAA
1 AAAGCCCACAAGTCAGTGGTAA-TCTTTTCAAAGTCCACACAAGTCGGTGGC-ACCCT-TTCAAA
* *
4349 GCCCACACAAGTCAATGGTACCC-TTTC
63 G-CC-CACAAGTCAGTGGCACCCTTTTC
* * * * *
4376 AAAGCCCACAAGTCAGTGGCACACCCTTTCAAAG--CTCTCAAGTCGGTGGCACCCTTTCAAAGC
1 AAAGCCCACAAGTCAGTGGTA-ATCTTTTCAAAGTCCACACAAGTCGGTGGCACCCTTTCAAAGC
4439 CCA
65 CCA
4442 TACAAGTCGA
Statistics
Matches: 368, Mismatches: 42, Indels: 25
0.85 0.10 0.06
Matches are distributed among these distances:
84 22 0.06
85 21 0.06
86 27 0.07
87 24 0.07
88 8 0.02
89 178 0.48
90 18 0.05
91 18 0.05
92 35 0.10
93 17 0.05
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (88 bp):
AAAGCCCACAAGTCAGTGGTAATCTTTTCAAAGTCCACACAAGTCGGTGGCACCCTTTCAAAGCC
CACAAGTCAGTGGCACCCTTTTC
Found at i:4264 original size:60 final size:59
Alignment explanation
Indices: 3934--4468 Score: 278
Period size: 60 Copynumber: 9.1 Consensus size: 59
3924 CGTCAATACG
* * * * * * * *
3934 AAAGCC-CACAAGTCAGTGGCATCCTTCTCATAGCCCACAAGTCAATGGC-A-TTTTTTC
1 AAAGCCACACAAGTCGGTAGCACCCTT-TTAAAGCCCACAAGTCAGTGACAACTCTTTTC
* * * * * * * *
3991 AAAGCC-CATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGC-A-TCCTTTC
1 AAAGCCACACAAGTCGGTAGCACCCTTTTAAAGCCCACAAGTCAGTGACAACTCTTTTC
* ** * * * *
4047 AAAGTC-CACAAGTCAATGGCATACCCTTTTAAAGCTCACAAGTCAGTGGC-ACCCTTTTC
1 AAAGCCACACAAGTCGGTAGC--ACCCTTTTAAAGCCCACAAGTCAGTGACAACTCTTTTC
* * * ** * * *
4106 AAAGCC-CACAAGTCAGTGGTAATTCTTTTCAAAGTCCACACAAGTCGGTGGC-AC-CCTTTC
1 AAAGCCACACAAGTCGGTAG-CACCCTTTT-AAAG-CC-CACAAGTCAGTGACAACTCTTTTC
* * * *
4166 AAAGCC-CATAAGTCTGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGATAACTCTTTTC
1 AAAGCCACACAAGTCGGTAGCACCCTTTT-AAAGCCCACAAGTCAGTGACAACTCTTTTC
* * *
4225 AAAGTCCACACAAGTTGGTAGCACCCTTTTAAAGCCCACAAGTCAGTGGC-ACCCTTTTC
1 AAAG-CCACACAAGTCGGTAGCACCCTTTTAAAGCCCACAAGTCAGTGACAACTCTTTTC
* * * * * *
4284 AAAGCC-CACAAGTCAGTGGTAACTCTTTTCAAAGTCCACACAAGTCGGTGGCAACT-TTGTTC
1 AAAGCCACACAAGTCGGTAG-CACCCTTTT-AAAG-CC-CACAAGTCAGTGACAACTCTT-TTC
** * * * * *
4346 AAAGCCCACACAAGTCAATGGTACCCTTTCAAAGCCCACAAGTCAGTGGCACAC-CCTTTC
1 AAAG-CCACACAAGTCGGTAGCACCCTTTTAAAGCCCACAAGTCAGTGACA-ACTCTTTTC
* * * *
4406 AAAG-CTCTCAAGTCGGTGGCACCCTTTCAAAGCCCATACAAGTC-GATGACAACTCTTTTC
1 AAAGCCACACAAGTCGGTAGCACCCTTTTAAAGCCC--ACAAGTCAG-TGACAACTCTTTTC
4466 AAA
1 AAA
4469 TCACCACTTT
Statistics
Matches: 394, Mismatches: 59, Indels: 47
0.79 0.12 0.09
Matches are distributed among these distances:
56 42 0.11
57 46 0.12
58 70 0.18
59 65 0.16
60 85 0.22
61 53 0.13
62 13 0.03
63 8 0.02
64 12 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (59 bp):
AAAGCCACACAAGTCGGTAGCACCCTTTTAAAGCCCACAAGTCAGTGACAACTCTTTTC
Found at i:4605 original size:49 final size:49
Alignment explanation
Indices: 4501--4667 Score: 182
Period size: 49 Copynumber: 3.5 Consensus size: 49
4491 GTCCGATATT
* * * *
4501 GCTGGCATTGAATCAGCATATTGG--CACCTTT--ATTAGCCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTC
*
4546 GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAACGTC
1 GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTC
* * * *
4595 ACTAGCCTTGAATCAGCACGTTAGTCCACTTTTCCCTATA-CCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCT-TAGCCCAATGTC
* * *
4644 GTTGGCCCTGAATTAGCACATTGG
1 GCTGGCCTTGAATCAGCACATTGG
4668 CTCCCTTCTT
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
45 22 0.22
47 6 0.06
49 70 0.70
50 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (49 bp):
GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTC
Found at i:5356 original size:20 final size:20
Alignment explanation
Indices: 5298--5356 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
5288 ATTTTTACCC
*
5298 CAATGTATCGATACATGT-GT
1 CAATGTATCGATACAT-TCTT
* *
5318 GAATGTAACGATACATTCTT
1 CAATGTATCGATACATTCTT
5338 CAATGTATCGATACATTCT
1 CAATGTATCGATACATTCT
5357 GTCTTTTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (20 bp):
CAATGTATCGATACATTCTT
Found at i:5421 original size:91 final size:91
Alignment explanation
Indices: 5298--5586 Score: 445
Period size: 91 Copynumber: 3.2 Consensus size: 91
5288 ATTTTTACCC
* *
5298 CAATGTATCGATACATGTGTGAATGTAACGATACATTCTTCAATGTATCGATACATTCTGTCTTT
1 CAATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTT
* *
5363 TTACCCAGATATATCGATAAATTTTT
66 TTACCCAGATGTATCGATACATTTTT
* * * *
5389 TAATGTATCAATATATGTATGAATGTATCGATACATTCTTCAATCTATCGATACATTCTGTCTTT
1 CAATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTT
*
5454 TCACCCAGATGTATCGATACATTTTT
66 TTACCCAGATGTATCGATACATTTTT
* * *
5480 CAATGTATCGATACATGTATGAATGTATCGATACATGT-ATGAATGTATCGATACATTCTATCTT
1 CAATGTATCGATACATGTATGAATGTATCGATACAT-TCTTCAATGTATCGATACATTCTGTCTT
*
5544 TTTACCCAGATGTATCGATACATTATT
65 TTTACCCAGATGTATCGATACATTTTT
5571 CAATGTATCGATACAT
1 CAATGTATCGATACAT
5587 TCTGTCTTTT
Statistics
Matches: 179, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
91 178 0.99
92 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (91 bp):
CAATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTT
TTACCCAGATGTATCGATACATTTTT
Found at i:5487 original size:20 final size:20
Alignment explanation
Indices: 5462--5535 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
5452 TTTCACCCAG
* * *
5462 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATGA
5482 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATGA
5502 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATGA
5522 ATGTATCGATACAT
1 ATGTATCGATACAT
5536 TCTATCTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATGTATGA
Found at i:5489 original size:51 final size:51
Alignment explanation
Indices: 5411--5637 Score: 280
Period size: 51 Copynumber: 4.7 Consensus size: 51
5401 ATATGTATGA
* * *
5411 ATGTATCGATACATTCTTCAATCTATCGATACATTCTGTCTTTTCACCCAG
1 ATGTATCGATACATTATTCAATGTATCGATACATTCTGTCTTTTTACCCAG
* **
5462 ATGTATCGATACATTTTTCAATGTATCGATACA---TG------TA-TGA-
1 ATGTATCGATACATTATTCAATGTATCGATACATTCTGTCTTTTTACCCAG
* *
5502 ATGTATCGATACATGTA-TGAATGTATCGATACATTCTATCTTTTTACCCAG
1 ATGTATCGATACAT-TATTCAATGTATCGATACATTCTGTCTTTTTACCCAG
*
5553 ATGTATCGATACATTATTCAATGTATCGATACATTCTGTCTTTTTACCTAG
1 ATGTATCGATACATTATTCAATGTATCGATACATTCTGTCTTTTTACCCAG
5604 ATGTATCGATACATTATTCAATGTATCGATACAT
1 ATGTATCGATACATTATTCAATGTATCGATACAT
5638 CTAGTTAAAA
Statistics
Matches: 150, Mismatches: 13, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
40 29 0.19
41 2 0.01
42 1 0.01
43 1 0.01
48 2 0.01
49 2 0.01
50 3 0.02
51 110 0.73
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (51 bp):
ATGTATCGATACATTATTCAATGTATCGATACATTCTGTCTTTTTACCCAG
Found at i:5499 original size:12 final size:12
Alignment explanation
Indices: 5482--5535 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
5472 ACATTTTTCA
5482 ATGTATCGATAC
1 ATGTATCGATAC
5494 ATGTAT-G--A-
1 ATGTATCGATAC
5502 ATGTATCGATAC
1 ATGTATCGATAC
5514 ATGTAT-G--A-
1 ATGTATCGATAC
5522 ATGTATCGATAC
1 ATGTATCGATAC
5534 AT
1 AT
5536 TCTATCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
8 12 0.35
9 4 0.12
11 4 0.12
12 14 0.41
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:10061 original size:16 final size:15
Alignment explanation
Indices: 10042--10090 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
10032 CACATTTATT
10042 TTTTTTCTCTTATTTC
1 TTTTTTC-CTTATTTC
*
10058 --TTTTCCTTATTGC
1 TTTTTTCCTTATTTC
10071 TTATTTTCCTT-TTTC
1 TT-TTTTCCTTATTTC
10086 TTTTT
1 TTTTT
10091 CCTCCATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 7 0.25
14 8 0.29
15 5 0.18
16 8 0.29
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTTTCCTTATTTC
Found at i:10092 original size:13 final size:14
Alignment explanation
Indices: 10037--10093 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
10027 CTTTTCACAT
10037 TTATTT-TTTTTCTC
1 TTATTTCTTTTTC-C
10051 TTATTTC-TTTTCC
1 TTATTTCTTTTTCC
*
10064 TTATTGCTTATTTTCC
1 TTATTTC-T-TTTTCC
10080 TT-TTTCTTTTTCC
1 TTATTTCTTTTTCC
10093 T
1 T
10094 CCATTCTGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 14 0.38
14 12 0.32
15 3 0.08
16 8 0.22
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.72
Consensus pattern (14 bp):
TTATTTCTTTTTCC
Found at i:10948 original size:15 final size:16
Alignment explanation
Indices: 10930--10967 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10920 AAAAATTATT
*
10930 AAATAATTAAAA-ATA
1 AAATAAGTAAAATATA
10945 AAATAAAGTAAAATATA
1 AAAT-AAGTAAAATATA
10962 AAATAA
1 AAATAA
10968 AGTTACAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 4 0.20
16 9 0.45
17 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAATAAGTAAAATATA
Found at i:10964 original size:17 final size:18
Alignment explanation
Indices: 10936--10980 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
10926 TATTAAATAA
10936 TTAAAA-ATAAAATAAAG
1 TTAAAATATAAAATAAAG
10953 -TAAAATATAAAATAAAG
1 TTAAAATATAAAATAAAG
*
10970 TTACAATATAA
1 TTAAAATATAA
10981 CTTTCTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 5 0.20
17 11 0.44
18 9 0.36
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
TTAAAATATAAAATAAAG
Found at i:16994 original size:13 final size:13
Alignment explanation
Indices: 16976--17002 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16966 GCATGCTGCT
16976 TTGTATCGATACA
1 TTGTATCGATACA
16989 TTGTATCGATACA
1 TTGTATCGATACA
17002 T
1 T
17003 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:17016 original size:32 final size:33
Alignment explanation
Indices: 16957--17021 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
16947 CACACCCAAA
* *
16957 TGTATCGATGCATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATGCTGCATTGTATCGATACAT
*
16990 TGTATCGATACATG-TTCATTGTATCGATACAT
1 TGTATCGATACATGCTGCATTGTATCGATACAT
17022 GGCCAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATGCTGCATTGTATCGATACAT
Found at i:17033 original size:21 final size:19
Alignment explanation
Indices: 16987--17043 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
16977 TGTATCGATA
**
16987 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGGC
17006 CATTGTATCGATACATGGC
1 CATTGTATCGATACATGGC
17025 CAAATTGTATCGATACATG
1 C--ATTGTATCGATACATG
17044 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGGC
Found at i:23423 original size:22 final size:21
Alignment explanation
Indices: 23398--23443 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
23388 ATCTTTTTAC
*
23398 AAATTCTTT-GTTTTTCACTTCA
1 AAATTCTTTCATTTTTCA--TCA
23420 AAA-TCTTTCATTTTTCATCA
1 AAATTCTTTCATTTTTCATCA
23440 AAAT
1 AAAT
23444 CATCAACAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 6 0.29
21 5 0.24
22 10 0.48
ACGTcount: A:0.30, C:0.17, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATTCTTTCATTTTTCATCA
Found at i:26726 original size:20 final size:20
Alignment explanation
Indices: 26689--26728 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
26679 ACCTCACTAG
26689 GTCGCGAACCAGCACCCCCA
1 GTCGCGAACCAGCACCCCCA
*
26709 GTCGC-AACCGGCAGCCCCCA
1 GTCGCGAACCAGCA-CCCCCA
26729 CACACAGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.23, C:0.50, G:0.23, T:0.05
Consensus pattern (20 bp):
GTCGCGAACCAGCACCCCCA
Done.