Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1988
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: 71818
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:4582 original size:3 final size:3
Alignment explanation
Indices: 4574--4622 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
4564 ATTCACCTCT
* *
4574 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4622 T
1 T
4623 ATAACTCAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:6232 original size:2 final size:2
Alignment explanation
Indices: 6225--6256 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6215 GAAGGAAAGA
6225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6257 TATGAAACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10033 original size:27 final size:28
Alignment explanation
Indices: 9991--10109 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 28
9981 TTTATTATAT
9991 TTTTATA-TTATAATTATA-TTTAAAATA
1 TTTTATATTTAT-ATTATATTTTAAAATA
**
10018 TTTTATATTTATATTA-ATTTTAGTATA
1 TTTTATATTTATATTATATTTTAAAATA
* * *
10045 TTAATAATTTTTATTATATAAATTTTAAAATA
1 TT--TTATATTTA-TAT-TATATTTTAAAATA
*
10077 ---TATATTTATATTATATTTT-AATTA
1 TTTTATATTTATATTATATTTTAAAATA
10101 TTTTATATT
1 TTTTATATT
10110 ATTATATTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
24 4 0.06
25 7 0.10
26 4 0.06
27 32 0.44
28 4 0.06
29 7 0.10
30 3 0.04
31 2 0.03
32 9 0.12
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTTATATTTATATTATATTTTAAAATA
Found at i:10119 original size:14 final size:14
Alignment explanation
Indices: 9985--10130 Score: 59
Period size: 13 Copynumber: 11.0 Consensus size: 14
9975 TACTTATTTA
*
9985 TTATATTTTTATA-
1 TTATATTATTATAT
9998 TTATA--ATTATAT
1 TTATATTATTATAT
10010 TTAAAATATT-TTATAT
1 TT---ATATTATTATAT
*
10026 TTATATTAATTTTA-
1 TTATATT-ATTATAT
* *
10040 GTATATTAATA-AT
1 TTATATTATTATAT
* *
10053 TTTTATTATATAAAT
1 TTATATTAT-TATAT
* *
10068 TT-TA-AAATATAT
1 TTATATTATTATAT
10080 ATT-TA-TATTATAT
1 -TTATATTATTATAT
10093 TT-TA--ATTAT-T
1 TTATATTATTATAT
10103 TTATATTATTATAT
1 TTATATTATTATAT
*
10117 TTATATAATTATAT
1 TTATATTATTATAT
10131 CATATTTAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
10 3 0.03
11 12 0.12
12 11 0.11
13 34 0.33
14 24 0.23
15 11 0.11
16 8 0.08
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.60
Consensus pattern (14 bp):
TTATATTATTATAT
Found at i:10155 original size:43 final size:41
Alignment explanation
Indices: 10075--10162 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 41
10065 AATTTTAAAA
* * *
10075 TATATATTTATATTATATTTTAATTATTTTATATTATTATATT
1 TATATAATTATATCATATTTTAATTATTTTAAATTATT-T-TT
10118 TATATAATTATATCATA-TTTAA-TATTATTAAATTTATTTTT
1 TATATAATTATATCATATTTTAATTATT-TTAAA-TTATTTTT
10159 TATA
1 TATA
10163 AATGTTACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 10 0.25
42 10 0.25
43 20 0.50
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (41 bp):
TATATAATTATATCATATTTTAATTATTTTAAATTATTTTT
Found at i:20665 original size:10 final size:10
Alignment explanation
Indices: 20650--20681 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
20640 TTGTACCAAC
20650 GAGAGAGATA
1 GAGAGAGATA
20660 GAGAGAGATA
1 GAGAGAGATA
*
20670 GAGAGAGGTA
1 GAGAGAGATA
20680 GA
1 GA
20682 CGTGATGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.44, T:0.09
Consensus pattern (10 bp):
GAGAGAGATA
Found at i:25148 original size:362 final size:362
Alignment explanation
Indices: 24483--25211 Score: 1458
Period size: 362 Copynumber: 2.0 Consensus size: 362
24473 AAAGTCTCCA
24483 AAGAACAATATCTGATGTATCGTTTGAACTAATAAGCAAAGAGAGAAGCCATTGATGCAAGTGCA
1 AAGAACAATATCTGATGTATCGTTTGAACTAATAAGCAAAGAGAGAAGCCATTGATGCAAGTGCA
24548 ACAACGCTTCCACGCATATCCGAAGTTGACGATGCCAGGGGTAAGTGCCGTGGCATGTCTGAAGA
66 ACAACGCTTCCACGCATATCCGAAGTTGACGATGCCAGGGGTAAGTGCCGTGGCATGTCTGAAGA
24613 GAGAAGAAGCACTCTTGAGCACTTAAGTCAAGTTCGAGACAAGTTCTCGAGGAAATTGCTCTGCG
131 GAGAAGAAGCACTCTTGAGCACTTAAGTCAAGTTCGAGACAAGTTCTCGAGGAAATTGCTCTGCG
24678 AGCGTTGTGCATCAATGAAGAAATGGAGAAGAAGAAGAATGGAGGCAAAGGCGAAGAAGCCTTAA
196 AGCGTTGTGCATCAATGAAGAAATGGAGAAGAAGAAGAATGGAGGCAAAGGCGAAGAAGCCTTAA
24743 CAGATCATATATGAATGCTCGTGTGATGTTCACCAGGCTTGGTCGAACTCACTCTGTGTTGTACC
261 CAGATCATATATGAATGCTCGTGTGATGTTCACCAGGCTTGGTCGAACTCACTCTGTGTTGTACC
24808 AAGCTGAGGCAACAAGAGAAATCCTGAAGAAGAGTTC
326 AAGCTGAGGCAACAAGAGAAATCCTGAAGAAGAGTTC
24845 AAGAACAATATCTGATGTATCGTTTGAACTAATAAGCAAAGAGAGAAGCCATTGATGCAAGTGCA
1 AAGAACAATATCTGATGTATCGTTTGAACTAATAAGCAAAGAGAGAAGCCATTGATGCAAGTGCA
24910 ACAACGCTTCCACGCATATCCGAAGTTGACGATGCCAGGGGTAAGTGCCGTGGCATGTCTGAAGA
66 ACAACGCTTCCACGCATATCCGAAGTTGACGATGCCAGGGGTAAGTGCCGTGGCATGTCTGAAGA
24975 GAGAAGAAGCACTCTTGAGCACTTAAGTCAAGTTCGAGACAAGTTCTCGAGGAAATTGCTCTGCG
131 GAGAAGAAGCACTCTTGAGCACTTAAGTCAAGTTCGAGACAAGTTCTCGAGGAAATTGCTCTGCG
25040 AGCGTTGTGCATCAATGAAGAAATGGAGAAGAAGAAGAATGGAGGCAAAGGCGAAGAAGCCTTAA
196 AGCGTTGTGCATCAATGAAGAAATGGAGAAGAAGAAGAATGGAGGCAAAGGCGAAGAAGCCTTAA
25105 CAGATCATATATGAATGCTCGTGTGATGTTCACCAGGCTTGGTCGAACTCACTCTGTGTTGTACC
261 CAGATCATATATGAATGCTCGTGTGATGTTCACCAGGCTTGGTCGAACTCACTCTGTGTTGTACC
25170 AAGCTGAGGCAACAAGAGAAATCCTGAAGAAGAGTTC
326 AAGCTGAGGCAACAAGAGAAATCCTGAAGAAGAGTTC
25207 AAGAA
1 AAGAA
25212 TAAGGGCTAA
Statistics
Matches: 367, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
362 367 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.21
Consensus pattern (362 bp):
AAGAACAATATCTGATGTATCGTTTGAACTAATAAGCAAAGAGAGAAGCCATTGATGCAAGTGCA
ACAACGCTTCCACGCATATCCGAAGTTGACGATGCCAGGGGTAAGTGCCGTGGCATGTCTGAAGA
GAGAAGAAGCACTCTTGAGCACTTAAGTCAAGTTCGAGACAAGTTCTCGAGGAAATTGCTCTGCG
AGCGTTGTGCATCAATGAAGAAATGGAGAAGAAGAAGAATGGAGGCAAAGGCGAAGAAGCCTTAA
CAGATCATATATGAATGCTCGTGTGATGTTCACCAGGCTTGGTCGAACTCACTCTGTGTTGTACC
AAGCTGAGGCAACAAGAGAAATCCTGAAGAAGAGTTC
Found at i:28325 original size:15 final size:16
Alignment explanation
Indices: 28287--28327 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
28277 TAATTATGTC
28287 ATATAAATATAATATA
1 ATATAAATATAATATA
* *
28303 ACAT-AATATAA-ATT
1 ATATAAATATAATATA
28317 ATATAAATATA
1 ATATAAATATA
28328 TTAAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.24
15 13 0.62
16 3 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAAATATAATATA
Found at i:37046 original size:18 final size:19
Alignment explanation
Indices: 37025--37060 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
37015 CAATTAATAA
37025 TAAATAAAAAATT-TAATT
1 TAAATAAAAAATTATAATT
*
37043 TAAATATAAAATTATAAT
1 TAAATAAAAAATTATAAT
37061 AAATACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATAAAAAATTATAATT
Found at i:37237 original size:23 final size:24
Alignment explanation
Indices: 37206--37250 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
37196 GATAAAATTT
37206 AAATATAAAATT-ATAAAAAATAAA
1 AAATAT-AAATTGATAAAAAATAAA
*
37230 AAAT-TAAATTGATATAAAATA
1 AAATATAAATTGATAAAAAATA
37251 CTAATTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATATAAATTGATAAAAAATAAA
Found at i:40849 original size:3 final size:3
Alignment explanation
Indices: 40843--40892 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
40833 AAAAAAAAGG
40843 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40890 TAT
1 TAT
40893 CTATCTATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40955 original size:4 final size:4
Alignment explanation
Indices: 40946--41016 Score: 71
Period size: 4 Copynumber: 19.0 Consensus size: 4
40936 GTTTGGCTGG
* * *
40946 GAAA GAAA GAAA GAAA GTAA GAAA -AAA -AAA GAAT GAAT GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
40991 GAAA AAAA GAAA -AAA -AAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
41017 AAAAATTATA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
3 15 0.26
4 43 0.74
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (4 bp):
GAAA
Found at i:40967 original size:12 final size:12
Alignment explanation
Indices: 40946--41016 Score: 71
Period size: 11 Copynumber: 6.3 Consensus size: 12
40936 GTTTGGCTGG
40946 GAAAGAAAGAAA
1 GAAAGAAAGAAA
*
40958 GAAAGTAAGAAA
1 GAAAGAAAGAAA
*
40970 -AAA-AAAGAAT
1 GAAAGAAAGAAA
*
40980 GAATGAAAG-AA
1 GAAAGAAAGAAA
*
40991 GAAAAAAAGAAA
1 GAAAGAAAGAAA
41003 -AAA-AAAGAAA
1 GAAAGAAAGAAA
41013 GAAA
1 GAAA
41017 AAAAATTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 12 0.25
11 19 0.40
12 17 0.35
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (12 bp):
GAAAGAAAGAAA
Found at i:40976 original size:22 final size:22
Alignment explanation
Indices: 40951--41021 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
40941 GCTGGGAAAG
*
40951 AAAGAAAGAAAGTAAGAAAAAA
1 AAAGAAAGAAAGAAAGAAAAAA
* *
40973 AAAGAATGAATGAAAGAAGAAAA
1 AAAGAAAGAAAGAAAGAA-AAAA
*
40996 AAAGAAAAAAAAAGAAAGAAAAAA
1 AAAG--AAAGAAAGAAAGAAAAAA
41020 AA
1 AA
41022 TTATATGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 15 0.38
23 8 0.20
24 6 0.15
25 11 0.28
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (22 bp):
AAAGAAAGAAAGAAAGAAAAAA
Found at i:41786 original size:16 final size:16
Alignment explanation
Indices: 41747--41787 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
41737 TTTTTATTAA
41747 AAATAATTAAAAATAT
1 AAATAATTAAAAATAT
* *
41763 AAAAAATTAAAAATGT
1 AAATAATTAAAAATAT
*
41779 AATTAATTA
1 AAATAATTA
41788 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
AAATAATTAAAAATAT
Found at i:42557 original size:19 final size:18
Alignment explanation
Indices: 42533--42581 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
42523 TACTCAGGTG
42533 AAAAAGAAAAAAAGAAACA
1 AAAAAGAAAAAAAGAAA-A
*
42552 AAAAAGCAAAAAAGAAAA
1 AAAAAGAAAAAAAGAAAA
*
42570 AAAAGGAAAAAA
1 AAAAAGAAAAAA
42582 TTTATGTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAGAAAA
Found at i:42688 original size:14 final size:15
Alignment explanation
Indices: 42664--42705 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
42654 TTTATTTGAT
*
42664 TTTATTTTATATATA
1 TTTATTATATATATA
42679 TTT-TTATATATA-A
1 TTTATTATATATATA
*
42692 TTTATTTTATATAT
1 TTTATTATATATAT
42706 GGGAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 16 0.70
15 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTATATATATA
Found at i:43865 original size:4 final size:4
Alignment explanation
Indices: 43858--43897 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
43848 ACGTGATGGA
*
43858 AAAG AAAG AAA- AAA- AAAG AAAG AAAG GAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
43898 AAAAAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 9 0.28
4 23 0.72
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:43906 original size:9 final size:9
Alignment explanation
Indices: 43856--43910 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
43846 TTACGTGATG
*
43856 GAAAAGAAA
1 GAAAAAAAA
43865 GAAAAAAAAA
1 G-AAAAAAAA
* *
43875 GAAAGAAAG
1 GAAAAAAAA
*
43884 GAAGAAAGAA
1 GAA-AAAAAA
43894 GAAAAAAAA
1 GAAAAAAAA
43903 GAAAAAAA
1 GAAAAAAA
43911 TTTATCAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
9 23 0.62
10 14 0.38
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:43974 original size:24 final size:25
Alignment explanation
Indices: 43947--44011 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 25
43937 TATTTGTATC
43947 TATATTTTTTTATA-CTTAAAATAT
1 TATATTTTTTTATATCTTAAAATAT
* * *
43971 TATATTTTTATATATTTTAACATAT
1 TATATTTTTTTATATCTTAAAATAT
43996 TAATAATTTATTTTAT
1 T-AT-ATTT-TTTTAT
44012 TTTATGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 13 0.39
25 9 0.27
26 2 0.06
27 4 0.12
28 5 0.15
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
TATATTTTTTTATATCTTAAAATAT
Found at i:44360 original size:2 final size:2
Alignment explanation
Indices: 44353--44382 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44343 TAATCTAATA
44353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44383 GAGTTACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52391 original size:2 final size:2
Alignment explanation
Indices: 52384--52420 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
52374 TCTCAAGGGG
*
52384 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GT GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
52421 GTTGATTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.51, T:0.03
Consensus pattern (2 bp):
GA
Found at i:52646 original size:16 final size:16
Alignment explanation
Indices: 52620--52658 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
52610 ATTAAAATTA
52620 AATATTAAAT-ATAATAT
1 AATA-TAAATAAT-ATAT
52637 AATATAAATAATATAT
1 AATATAAATAATATAT
52653 AATATA
1 AATATA
52659 TCAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAAATAATATAT
Found at i:52673 original size:16 final size:15
Alignment explanation
Indices: 52654--52704 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
52644 ATAATATATA
*
52654 ATATATCAAAATTTAT
1 ATATAT-AAATTTTAT
52670 ATATTATAAATTATTA-
1 ATA-TATAAATT-TTAT
52686 ATATATTAAATTTTAT
1 ATATA-TAAATTTTAT
52702 ATA
1 ATA
52705 AATATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 5 0.17
16 19 0.63
17 6 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATAAATTTTAT
Found at i:53473 original size:20 final size:19
Alignment explanation
Indices: 53448--53486 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
53438 TTAAAAAATT
*
53448 ATATATAAATCAAATTAAAA
1 ATATATAAAT-AAAATAAAA
*
53468 ATATATTAATAAAATAAAA
1 ATATATAAATAAAATAAAA
53487 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
ATATATAAATAAAATAAAA
Found at i:53482 original size:25 final size:26
Alignment explanation
Indices: 53445--53500 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
53435 AATTTAAAAA
*
53445 ATTATATATAAATCAAATTAAAAATAT
1 ATTA-ATATAAATAAAATTAAAAATAT
53472 ATTAATA-AAATAAAATTAAAAATAT
1 ATTAATATAAATAAAATTAAAAATAT
53497 -TTAA
1 ATTAA
53501 ATATTTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 4 0.14
25 17 0.61
26 3 0.11
27 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
ATTAATATAAATAAAATTAAAAATAT
Found at i:53503 original size:25 final size:26
Alignment explanation
Indices: 53438--53504 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
53428 CTAATTTAAT
* *
53438 TTAAAAA-A-TTATATATAAATCAAA
1 TTAAAAATATTTAAATATAAATAAAA
53462 TTAAAAATATATT-AATA-AAATAAAA
1 TTAAAAATAT-TTAAATATAAATAAAA
53487 TTAAAAATATTTAAATAT
1 TTAAAAATATTTAAATAT
53505 TTCAATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
24 9 0.25
25 22 0.61
26 3 0.08
27 2 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (26 bp):
TTAAAAATATTTAAATATAAATAAAA
Found at i:54255 original size:18 final size:20
Alignment explanation
Indices: 54228--54269 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
54218 AAATAAAATA
*
54228 ATTACAATTT-TA-TTTTTT
1 ATTACAATTTATACATTTTT
*
54246 ATTACTATTTATACATTTTT
1 ATTACAATTTATACATTTTT
54266 ATTA
1 ATTA
54270 TTTAAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTACAATTTATACATTTTT
Found at i:56893 original size:31 final size:29
Alignment explanation
Indices: 56856--56924 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
56846 ATTTGACAAT
*
56856 ATAAAATAATTAAAATATAATATATAATATA
1 ATAAAATAATTAAAA-ATAATATA-AATAAA
*
56887 ATAAAAT-TTTAAAAATAATATAAATAAA
1 ATAAAATAATTAAAAATAATATAAATAAA
56915 ATATAAATAA
1 ATA-AAATAA
56925 ATAATTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 8 0.24
29 12 0.36
30 6 0.18
31 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
ATAAAATAATTAAAAATAATATAAATAAA
Found at i:56933 original size:14 final size:13
Alignment explanation
Indices: 56853--56940 Score: 53
Period size: 14 Copynumber: 7.0 Consensus size: 13
56843 TAGATTTGAC
*
56853 AATATAAAATAATT
1 AATAT-AAATAAAT
* *
56867 AAAATATAATATAT
1 AATATA-AATAAAT
56881 AATAT-AAT-AA-
1 AATATAAATAAAT
* *
56891 AATTTTAA-AAAT
1 AATATAAATAAAT
56903 AATATAAAT-AA-
1 AATATAAATAAAT
56914 AATATAAATAAAT
1 AATATAAATAAAT
*
56927 AATTATATATAAAT
1 AA-TATAAATAAAT
56941 TCATATTATA
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
10 4 0.07
11 14 0.25
12 13 0.23
13 3 0.05
14 23 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATATAAATAAAT
Found at i:57955 original size:18 final size:18
Alignment explanation
Indices: 57932--57966 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57922 ATCGAATTAT
57932 AAAAAAATTATATTAATC
1 AAAAAAATTATATTAATC
*
57950 AAAAAAATTATTTTAAT
1 AAAAAAATTATATTAAT
57967 TAATTTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAAAATTATATTAATC
Found at i:61264 original size:15 final size:14
Alignment explanation
Indices: 61217--61266 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 14
61207 TATATATTTA
61217 TTTTTTAAAATATAT
1 TTTTTTAAAAT-TAT
*
61232 TTTATTAAATACTTAT
1 TTTTTTAAA-A-TTAT
61248 TTTTTTATAAATTAT
1 TTTTTTA-AAATTAT
61263 TTTT
1 TTTT
61267 ATTTCACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 16 0.53
16 11 0.37
17 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTAAAATTAT
Found at i:61522 original size:18 final size:18
Alignment explanation
Indices: 61499--61541 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
61489 AATTAAGTGA
*
61499 TAAATTATTTTAAAATTT
1 TAAATTATTTAAAAATTT
*
61517 TAAATTAATTAAAAATTT
1 TAAATTATTTAAAAATTT
61535 T-AATTAT
1 TAAATTAT
61542 AATACCTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAATTATTTAAAAATTT
Found at i:65442 original size:30 final size:29
Alignment explanation
Indices: 65398--65467 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
65388 ATCTATTTTA
65398 ATTTAAAT-ATAAAAT-ATTTTTTAATATT
1 ATTTAAATAATAAAATAATTTTTTAAT-TT
65426 ATTTTAAATAATAAAATAAATTTTTTAATTT
1 A-TTTAAATAATAAAAT-AATTTTTTAATTT
*
65457 ACTTAAATAAT
1 ATTTAAATAAT
65468 TTAAATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 7 0.19
30 16 0.43
31 3 0.08
32 10 0.27
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTAAATAATAAAATAATTTTTTAATTT
Found at i:67758 original size:3 final size:3
Alignment explanation
Indices: 67750--67790 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
67740 GATCTCTTTT
67750 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
67791 GCGACGATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.