Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2138
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: 16824
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:3184 original size:13 final size:13
Alignment explanation
Indices: 3166--3225 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
3156 CCTTCTCTTC
*
3166 AAAAAAGAAAGCAA
1 AAAAAAAAAAGC-A
*
3180 AAAAAAAAAAGGA
1 AAAAAAAAAAGCA
3193 AAAAAACAAAA-CA
1 AAAAAA-AAAAGCA
*
3206 AAAAACAAAA-CA
1 AAAAAAAAAAGCA
3218 AAGAAAAA
1 AA-AAAAA
3226 GAGAGAAAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 8 0.21
13 17 0.44
14 14 0.36
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGCA
Found at i:3186 original size:15 final size:14
Alignment explanation
Indices: 3166--3215 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3156 CCTTCTCTTC
*
3166 AAAAAAGAAAGCAA
1 AAAAAAAAAAGCAA
*
3180 AAAAAAAAAAGGAA
1 AAAAAAAAAAGCAA
*
3194 AAAAACAAAA-CAA
1 AAAAAAAAAAGCAA
3207 AAAACAAAA
1 AAAA-AAAA
3216 CAAAGAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 6 0.20
14 24 0.80
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGCAA
Found at i:3198 original size:27 final size:29
Alignment explanation
Indices: 3166--3225 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
3156 CCTTCTCTTC
* * *
3166 AAAAAAGAAAGCAAAAAA-AAAA-AAGGA
1 AAAAAACAAAACAAAAAACAAAACAAAGA
3193 AAAAAACAAAACAAAAAACAAAACAAAGA
1 AAAAAACAAAACAAAAAACAAAACAAAGA
3222 AAAA
1 AAAA
3226 GAGAGAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 16 0.57
28 4 0.14
29 8 0.29
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (29 bp):
AAAAAACAAAACAAAAAACAAAACAAAGA
Found at i:3208 original size:12 final size:12
Alignment explanation
Indices: 3193--3219 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3183 AAAAAAAGGA
3193 AAAAAACAAAAC
1 AAAAAACAAAAC
3205 AAAAAACAAAAC
1 AAAAAACAAAAC
3217 AAA
1 AAA
3220 GAAAAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:4350 original size:59 final size:59
Alignment explanation
Indices: 4208--4634 Score: 523
Period size: 59 Copynumber: 7.3 Consensus size: 59
4198 TCCGCTTTTT
* * * * **
4208 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAAGCCCCCACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACG-CTTTTTCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-C
4270 AGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
4329 AGTCCTCAAAGAGCGGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
4388 AGTCCTCAAAGAGCAGGACACATTTTCTCTTAAAGCCCACACAAGTTGGTAGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
4447 AGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCCCACACAAGTTGATGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* ** **
4506 AGTCCTCAAAGAGTAGGAC-C-CCTT-TC--AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-C
* * * * * **
4561 AGTCCTCAAAGAGCAAGACAC--CTT-TC--AAAGCCCACATAAGTTGATGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-C
4616 AGTCCTCAAAGAGCAGGAC
1 AGTCCTCAAAGAGCAGGAC
4635 ACCCCTCAAA
Statistics
Matches: 337, Mismatches: 26, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
54 24 0.07
55 68 0.20
56 3 0.01
57 2 0.01
58 1 0.00
59 187 0.55
60 24 0.07
61 9 0.03
62 19 0.06
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (59 bp):
AGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:4659 original size:74 final size:74
Alignment explanation
Indices: 4564--4707 Score: 209
Period size: 74 Copynumber: 1.9 Consensus size: 74
4554 ATTTTCCAGT
*
4564 CCTCAAAGAGCAAGACACCTTTCAAAGCCCACATAAGTTGATGGCA-TTTTCCAGTCCTCAAAGA
1 CCTCAAAGAGCAAGACACCTTTCAAAGCCCACACAAGTTGATGGCACTTTT-CAGTCCTCAAAGA
4628 GCAGGACACC
65 GCAGGACACC
* ** * * *
4638 CCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAG
1 CCTCAAAGAGCAAGACACCTTTCAAAGCCCACACAAGTTGATGGCACTTTTCAGTCCTCAAAGAG
4703 CAGGA
66 CAGGA
4708 TACACTTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 58 0.94
75 4 0.06
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (74 bp):
CCTCAAAGAGCAAGACACCTTTCAAAGCCCACACAAGTTGATGGCACTTTTCAGTCCTCAAAGAG
CAGGACACC
Found at i:5464 original size:21 final size:21
Alignment explanation
Indices: 5438--5514 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
5428 AAAAAATTCA
5438 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
5459 AATGTATCGAAACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
5480 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
5501 AATGTATCGATACA
1 AATGTATCGATACA
5515 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:5574 original size:19 final size:19
Alignment explanation
Indices: 5550--5617 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
5540 AATTCAACAA
5550 TTTGTATCGATACATAAAT
1 TTTGTATCGATACATAAAT
5569 TTTGTATCGATAC---AA-
1 TTTGTATCGATACATAAAT
*
5584 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAAT
*
5601 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
5618 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
16 3 0.07
19 28 0.67
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAAT
Found at i:5589 original size:13 final size:13
Alignment explanation
Indices: 5571--5595 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5561 ACATAAATTT
5571 TGTATCGATACAA
1 TGTATCGATACAA
5584 TGTATCGATACA
1 TGTATCGATACA
5596 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5593 original size:32 final size:32
Alignment explanation
Indices: 5552--5614 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
5542 TTCAACAATT
*
5552 TGTATCGATACATAAATTTTGTATCGATACAA
1 TGTATCGATACATAAATATTGTATCGATACAA
*
5584 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAATATTGTATCGATACA
5615 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAATATTGTATCGATACAA
Found at i:5661 original size:20 final size:20
Alignment explanation
Indices: 5636--5691 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5626 TGCCAAGGAA
*
5636 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTATCT
**
5656 ATGTATCGATACATGGATCT
1 ATGTATCGATACATTTATCT
*
5676 TTGTATCGATACATTT
1 ATGTATCGATACATTT
5692 GGAAATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTATCT
Found at i:8268 original size:51 final size:51
Alignment explanation
Indices: 8205--8371 Score: 199
Period size: 52 Copynumber: 3.2 Consensus size: 51
8195 TTTTCGAGGA
* * ***
8205 GATACTCTAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATCGGG
* * * * *
8256 GATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTCAATCGGG
1 GATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCAT-AATCGGG
* * *
8308 GATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAG
1 GATACTCCAACCCCGATTTTATTTCC-AAAATACCAATTTTTCATAATCGGG
8360 GATACTCCAACC
1 GATACTCCAACC
8372 TCGTTATTTC
Statistics
Matches: 95, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
51 34 0.36
52 47 0.49
53 14 0.15
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.32
Consensus pattern (51 bp):
GATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATCGGG
Found at i:8328 original size:52 final size:53
Alignment explanation
Indices: 8037--8371 Score: 201
Period size: 51 Copynumber: 6.4 Consensus size: 53
8027 CAATTCTCCA
* * * *
8037 CAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAATTTT-CTAT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCT-T
* *
8089 -AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAA-TTTCTTT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAAACACCAATTTTCCTT
* * * *** * * **
8141 ACAATCGGGGACACTCCAACCCCG--TTAATCATCGGGGATACTCCAA--CCCCGTT
1 -CAATCGGGGATACTCCAACCCCGATTTTAT-TTC-CAAAAACACCAATTTTCC-TT
* * * * *** * *
8194 -ATTTTCGAGGAGATACTCTAACCCCGACTTTATTTCC-AAAATATTGATTTTTCAT
1 CA--ATCG-GG-GATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
* *
8249 -AATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
* * * *
8300 CAATCGGGGATACTCCAACACCGATTTTATTTCCAAAAATACCAATTTTTC-A
1 CAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
*
8352 CAATCGAGGATACTCCAACC
1 CAATCGGGGATACTCCAACC
8372 TCGTTATTTC
Statistics
Matches: 213, Mismatches: 52, Indels: 36
0.71 0.17 0.12
Matches are distributed among these distances:
51 66 0.31
52 59 0.28
53 41 0.19
54 25 0.12
55 15 0.07
56 3 0.01
57 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (53 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTT
Found at i:8405 original size:28 final size:28
Alignment explanation
Indices: 8354--8435 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
8344 ATTTTTCACA
*
8354 ATCGAGGATACTCCAA-CCTCGTTATTTC
1 ATCGGGGATACTCCAACCCT-GTTATTTC
*
8382 ATCGGGGATACTCCAACCCTGTTACTTC
1 ATCGGGGATACTCCAACCCTGTTATTTC
* *
8410 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCTGTTATT
8436 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 38 0.83
29 3 0.07
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCTGTTATTTC
Found at i:8430 original size:211 final size:211
Alignment explanation
Indices: 8038--8430 Score: 578
Period size: 211 Copynumber: 1.9 Consensus size: 211
8028 AATTCTCCAC
* * *
8038 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* * *
8103 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTTACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
* * * *
8168 ATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCTAACCCCGACTTTATTTCCAA
131 ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGAGACACTCCAACCCCGACTTTATTTCCAA
8233 AATATTGATTTTTCAT
196 AATATTGATTTTTCAT
*
8249 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCT-TCAATCGGGGATAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTAT-AATCGGGGATAC
* * *
8313 TCCAACACCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCGT
64 TCCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGT
* *
8376 TATTTCATCGGGGATACTCCAACCCTGTTACTTCCGAGG-GAACACTCCAACCCCG
129 TA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGAG-ACACTCCAACCCCG
8431 TTATTATCTC
Statistics
Matches: 162, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
210 27 0.17
211 101 0.62
212 34 0.21
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (211 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGAGACACTCCAACCCCGACTTTATTTCCAA
AATATTGATTTTTCAT
Found at i:10132 original size:19 final size:19
Alignment explanation
Indices: 10108--10204 Score: 110
Period size: 19 Copynumber: 5.7 Consensus size: 19
10098 GTCAACGATT
10108 TGTATCGATACATAAGTGC
1 TGTATCGATACATAAGTGC
10127 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGC
10140 TGTATCGATACATAAGTGC
1 TGTATCGATACATAAGTGC
10159 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGC
10172 TGTATCGATACATAAGTGC
1 TGTATCGATACATAAGTGC
10191 TGTATCGATACATA
1 TGTATCGATACATA
10205 TGAAGCTATT
Statistics
Matches: 66, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 36 0.55
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (19 bp):
TGTATCGATACATAAGTGC
Found at i:10144 original size:32 final size:32
Alignment explanation
Indices: 10108--10202 Score: 190
Period size: 32 Copynumber: 3.0 Consensus size: 32
10098 GTCAACGATT
10108 TGTATCGATACATAAGTGCTGTATCGATACAA
1 TGTATCGATACATAAGTGCTGTATCGATACAA
10140 TGTATCGATACATAAGTGCTGTATCGATACAA
1 TGTATCGATACATAAGTGCTGTATCGATACAA
10172 TGTATCGATACATAAGTGCTGTATCGATACA
1 TGTATCGATACATAAGTGCTGTATCGATACA
10203 TATGAAGCTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATAAGTGCTGTATCGATACAA
Found at i:10145 original size:13 final size:13
Alignment explanation
Indices: 10127--10183 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
10117 ACATAAGTGC
10127 TGTATCGATACAA
1 TGTATCGATACAA
10140 TGTATCGATACATAA
1 TGTATCGATAC--AA
10155 GTGCTGTATCGATACAA
1 ----TGTATCGATACAA
10172 TGTATCGATACA
1 TGTATCGATACA
10184 TAAGTGCTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:10250 original size:20 final size:19
Alignment explanation
Indices: 10225--10278 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
10215 GCCAAGAAAA
*
10225 TGTATCGATACATTACTCAT
1 TGTATCGATACATGA-TCAT
*
10245 TGTATCGATACACTGATCTT
1 TGTATCGATACA-TGATCAT
10265 TGTATCGATACATG
1 TGTATCGATACATG
10279 CAGGCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:14381 original size:201 final size:201
Alignment explanation
Indices: 14015--14416 Score: 662
Period size: 201 Copynumber: 2.0 Consensus size: 201
14005 TATATCTTTT
* *
14015 TACAATTGGGTCCACAATATGAAAAATAAGTGGATAGGTATTTTTGAACAAATAAGAAGCTTTTT
1 TACAATTGGGTCCACAATATGAAAAATAAGTGGATAAGTATTTTTGAACAAATAAAAAGCTTTTT
* *
14080 AAAAAGTATCAAAATAAATTTGGGGAGCATCAACTTGTTTCATCTAGTGATGTTGAAAGAAATAG
66 AAAAAGTATCAAAATAAATTTGGGGAGCATCAACTTGCTTCATCTAGTGATGCTGAAAGAAATAG
* * *
14145 TCAATGAGAAATTTGTCAAGGAATGAGAATAAGTTATATTTGTTTACATTTTTATTAAATTATTA
131 TCAAAGAAAAATTTCTCAAGGAATGAGAATAAGTTATATTTGTTTACATTTTTATTAAATTATTA
14210 ATTAAA
196 ATTAAA
* * *
14216 TACAATTGGGTTCACAATATG-AAAATAATTGGGTAAGTATTTTTGAACAAATGAAAAAGCTTTT
1 TACAATTGGGTCCACAATATGAAAAATAAGTGGATAAGTATTTTTGAACAAAT-AAAAAGCTTTT
* *
14280 TGAAAAGTATCGAAATAAATTTGGGGAGCATCAACTTGCTTCATCTAGTGATGCTGAAAGAAATA
65 TAAAAAGTATCAAAATAAATTTGGGGAGCATCAACTTGCTTCATCTAGTGATGCTGAAAGAAATA
* *
14345 GTCAAAGAAAAATTTCTCAAGGCATGAGAGTAAGTTATATTTGTTTACATTTTTATTAAATTATT
130 GTCAAAGAAAAATTTCTCAAGGAATGAGAATAAGTTATATTTGTTTACATTTTTATTAAATTATT
14410 AATTAAA
195 AATTAAA
14417 GATTTTAATA
Statistics
Matches: 186, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
200 28 0.15
201 158 0.85
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (201 bp):
TACAATTGGGTCCACAATATGAAAAATAAGTGGATAAGTATTTTTGAACAAATAAAAAGCTTTTT
AAAAAGTATCAAAATAAATTTGGGGAGCATCAACTTGCTTCATCTAGTGATGCTGAAAGAAATAG
TCAAAGAAAAATTTCTCAAGGAATGAGAATAAGTTATATTTGTTTACATTTTTATTAAATTATTA
ATTAAA
Found at i:15398 original size:22 final size:22
Alignment explanation
Indices: 15373--15416 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
15363 TAAAGCTCAT
15373 GATATAATTCACTTTTTGATAA
1 GATATAATTCACTTTTTGATAA
15395 GATATAATTCACTTTTTGATAA
1 GATATAATTCACTTTTTGATAA
15417 ATTATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (22 bp):
GATATAATTCACTTTTTGATAA
Found at i:15698 original size:15 final size:16
Alignment explanation
Indices: 15667--15700 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
15657 TTCTTTCGGG
15667 TTGAGCTATTTCGAGT
1 TTGAGCTATTTCGAGT
15683 TTGAGCTATTTC-AGT
1 TTGAGCTATTTCGAGT
15698 TTG
1 TTG
15701 GATTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (16 bp):
TTGAGCTATTTCGAGT
Found at i:16141 original size:20 final size:21
Alignment explanation
Indices: 16116--16167 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
16106 TCTTAAAAAT
*
16116 TTTTATTTATATTTT-ATTTA-
1 TTTTATTTAT-TTTTAAATTAG
16136 TTTTA-TTATTTTTAAATTAG
1 TTTTATTTATTTTTAAATTAG
16156 TTTTATTTATTT
1 TTTTATTTATTT
16168 ATTTTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.14
19 8 0.29
20 10 0.36
21 6 0.21
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTATTTATTTTTAAATTAG
Found at i:16706 original size:20 final size:20
Alignment explanation
Indices: 16681--16727 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
16671 CAATGCTTCA
16681 ATTGATTACCTACTAATTAG
1 ATTGATTACCTACTAATTAG
* *
16701 ATTGATTATCTATTAATTAG
1 ATTGATTACCTACTAATTAG
16721 ATTGATT
1 ATTGATT
16728 TGATAATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.47
Consensus pattern (20 bp):
ATTGATTACCTACTAATTAG
Done.